TheSeed seedwiki http:/// /wiki/Main_Page MediaWiki 1.35.6 first-letter Media Special Talk User User talk TheSeed TheSeed talk File File talk MediaWiki MediaWiki talk Template Template talk Help Help talk Category Category talk 0 1 1 2006-07-31T18:04:46Z MediaWiki default 0 wikitext text/x-wiki <big>'''MediaWiki has been successfully installed.'''</big> Consult the [http://meta.wikipedia.org/wiki/MediaWiki_User%27s_Guide User's Guide] for information on using the wiki software. == Getting started == * [http://www.mediawiki.org/wiki/Help:Configuration_settings Configuration settings list] * [http://www.mediawiki.org/wiki/Help:FAQ MediaWiki FAQ] * [http://mail.wikipedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list] cfe9e457290978db5c59f7ed0e6495177716a20e 1367 1 2006-08-01T14:55:52Z FolkerMeyer 2 wikitext text/x-wiki == '''Home of the SEED''' == Consult the [http://meta.wikipedia.org/wiki/MediaWiki_User%27s_Guide User's Guide] for information on using the wiki software. == Getting started == * [http://www.mediawiki.org/wiki/Help:Configuration_settings Configuration settings list] * [http://www.mediawiki.org/wiki/Help:FAQ MediaWiki FAQ] * [http://mail.wikipedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list] 60856b2e479c1e4346c5384802f3a4f81f0eb784 1368 1367 2006-08-01T14:59:42Z FolkerMeyer 2 wikitext text/x-wiki == '''Home of the SEED''' == With the growing number of genomes becoming available, a software environment is needed to produce accurate and consistent annotations. The SEED is that environment. The annotation is performed not on a gene by gene basis per genome, but rather by subsystem by an expert curator across many genomes at a time. You can download software and data from our [[Download]] page. 5fd59c6a15f5c3794a3f2f363617d722768a5b8a 1372 1368 2006-08-01T15:08:01Z FolkerMeyer 2 wikitext text/x-wiki == '''Home of the SEED''' == With the growing number of genomes becoming available, a software environment is needed to produce accurate and consistent annotations. The SEED is that environment. The annotation is performed not on a gene by gene basis per genome, but rather by subsystem by an expert curator across many genomes at a time. * You can download software and data from our [[Download]] page. * We provide a list [[Glossary]] of terms used. 938387ed07ffc2561588fc30562ebe2ee48b9915 1376 1372 2006-08-01T15:22:33Z FolkerMeyer 2 wikitext text/x-wiki == '''Home of the SEED''' == With the growing number of genomes becoming available, a software environment is needed to produce accurate and consistent annotations. The SEED is that environment, we provide a [http://www.theseed.org/FIG/index.cgi read-only copy of the SEED] environment with the latest data and annotations. For users interested in editing and learning how to use the system, we also provide a [http://theseed.uchicago.edu/FIG/index.cgi public SEED]. The annotation is performed not on a gene by gene basis per genome, but rather by subsystem by an expert curator across many genomes at a time. * You can download software and data from our [[Download]] page. * We provide a list [[Glossary]] of terms used. 2b4043e28a90b104e5cc2fb8f3b4f11296c103e5 1377 1376 2006-08-01T15:27:10Z FolkerMeyer 2 wikitext text/x-wiki == '''Home of the SEED''' == With the growing number of genomes becoming available, a software environment is needed to produce accurate and consistent annotations. The SEED is that environment, we provide a [http://www.theseed.org/FIG/index.cgi read-only copy of the SEED] environment with the latest data and annotations. For users interested in editing and learning how to use the system, we also provide a [http://theseed.uchicago.edu/FIG/index.cgi public SEED]. The [[Glossary#annotation|annoation]] is performed not on a gene by gene basis per genome, but rather by [[Glossary#subsystem|subsystem]] by an expert curator across many genomes at a time. * You can download software and data from our [[Download]] page. * We provide a list [[Glossary]] of terms used. * When using the SEED, please cite: Overbeek et al., The Subsystems Approach to Genome Annotation and its Use in the Project to Annotate 1000 Genomes Nucleic Acids Res 33(17), 2005 e9cf53e452b91222d18b6e7954066e95505c5b4f 1378 1377 2006-08-01T15:28:53Z FolkerMeyer 2 wikitext text/x-wiki == '''Home of the SEED''' == With the growing number of genomes becoming available, a software environment is needed to produce accurate and consistent annotations. The SEED is that environment, we provide a [http://www.theseed.org/FIG/index.cgi read-only copy of the SEED] environment with the latest data and annotations. For users interested in editing and learning how to use the system, we also provide a [http://theseed.uchicago.edu/FIG/index.cgi public SEED]. The [[Glossary#annotation|annoation]] is performed not on a gene by gene basis per genome, but rather by [[Glossary#subsystem|subsystem]] by an expert curator across many genomes at a time. * You can download software and data from our [[Download]] page. * We provide a list [[Glossary]] of terms used. * When using the SEED, please cite: Overbeek et al., The Subsystems Approach to Genome Annotation and its Use in the Project to Annotate 1000 Genomes, [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16214803&query_hl=2&itool=pubmed_docsum|Nucleic Acids Res 33(17)], 2005 54991364118a8ad021b4d824b02308628b2b62f5 1379 1378 2006-08-01T15:39:41Z FolkerMeyer 2 wikitext text/x-wiki == '''Home of the SEED''' == With the growing number of genomes becoming available, a software environment is needed to produce accurate and consistent annotations. The SEED is that environment, we provide a [http://www.theseed.org/FIG/index.cgi read-only copy of the SEED] environment with the latest data and annotations. For users interested in editing and learning how to use the system, we also provide a [http://theseed.uchicago.edu/FIG/index.cgi public SEED]. The [[Glossary#annotation|annoation]] is performed not on a gene by gene basis per genome, but rather by [[Glossary#subsystem|subsystem]] by an expert curator across many genomes at a time. * You can download software and data from our [[Download]] page. * We provide a list [[Glossary]] of terms used. * When using the SEED, please cite: Overbeek et al., [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16214803&query_hl=2&itool=pubmed_docsum|Nucleic Acids Res 33(17)], 2005 * Ross Overbeek laid out the strategy for the annotation of the first 1000 genomes in [[Annotating_1000_genomes|here] 1864244ecece708b20d4890b47a0a2c8bd67cd63 1380 1379 2006-08-01T15:39:49Z FolkerMeyer 2 wikitext text/x-wiki == '''Home of the SEED''' == With the growing number of genomes becoming available, a software environment is needed to produce accurate and consistent annotations. The SEED is that environment, we provide a [http://www.theseed.org/FIG/index.cgi read-only copy of the SEED] environment with the latest data and annotations. For users interested in editing and learning how to use the system, we also provide a [http://theseed.uchicago.edu/FIG/index.cgi public SEED]. The [[Glossary#annotation|annoation]] is performed not on a gene by gene basis per genome, but rather by [[Glossary#subsystem|subsystem]] by an expert curator across many genomes at a time. * You can download software and data from our [[Download]] page. * We provide a list [[Glossary]] of terms used. * When using the SEED, please cite: Overbeek et al., [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16214803&query_hl=2&itool=pubmed_docsum|Nucleic Acids Res 33(17)], 2005 * Ross Overbeek laid out the strategy for the annotation of the first 1000 genomes in [[Annotating_1000_genomes|here]] db6b5c469110f0ad72c2d873ab68ce470d753c2f 1387 1380 2006-08-01T20:25:38Z FolkerMeyer 2 wikitext text/x-wiki == '''Home of the SEED''' == With the growing number of genomes becoming available, a software environment is needed to produce accurate and consistent annotations. The SEED is that environment, we provide a [http://www.theseed.org/FIG/index.cgi read-only copy of the SEED] environment with the latest data and annotations. For users interested in editing and learning how to use the system, we also provide a [http://theseed.uchicago.edu/FIG/index.cgi public SEED]. The [[Glossary#annotation|annoation]] is performed not on a gene by gene basis per genome, but rather by [[Glossary#subsystem|subsystem]] by an expert curator across many genomes at a time. * You can download software and data from our [[Download]] page. * We provide a list [[Glossary]] of terms used. * When using the SEED, please cite: Overbeek et al., [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16214803&query_hl=2&itool=pubmed_docsum|Nucleic Acids Res 33(17)], 2005 * Ross Overbeek laid out the [[Annotating_1000_genomes|strategy]] for the annotation of the first 1000 genomes. * Our approaches to annotation, gene calling etc are outlined in a series of [[SOPs|Standard Operating Procedures]]. 71d3c19b35aca8db050e9f75d6e8a91b4add03ac 1389 1387 2006-08-01T21:07:44Z WilliamMihalo 3 /* '''Home of the SEED''' */ wikitext text/x-wiki == '''Home of the SEED''' == With the growing number of genomes becoming available, a software environment is needed to produce accurate and consistent annotations. The SEED is that environment, we provide a [http://www.theseed.org/FIG/index.cgi read-only copy of the SEED] environment with the latest data and annotations. For users interested in editing and learning how to use the system, we also provide a [http://theseed.uchicago.edu/FIG/index.cgi public SEED]. The [[Glossary#annotation|annotation]] is performed not on a gene by gene basis per genome, but rather by [[Glossary#subsystem|subsystem]] by an expert curator across many genomes at a time. * You can download software and data from our [[Download]] page. * We provide a list [[Glossary]] of terms used. * When using the SEED, please cite: Overbeek et al., [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16214803&query_hl=2&itool=pubmed_docsum|Nucleic Acids Res 33(17)], 2005 * Ross Overbeek laid out the [[Annotating_1000_genomes|strategy]] for the annotation of the first 1000 genomes. * Our approaches to annotation, gene calling etc are outlined in a series of [[SOPs|Standard Operating Procedures]]. 3c4e23e25abfb3940e3bdd17d860760b068c417c 1396 1389 2006-08-11T17:30:07Z FolkerMeyer 2 wikitext text/x-wiki == '''Home of the SEED''' == With the growing number of genomes becoming available, a software environment is needed to produce accurate and consistent annotations. The SEED is that environment, we provide a public [http://www.theseed.org/FIG/index.cgi Viewing SEED] that allows read-only access to the latest data and annotations. For users interested in editing and learning how to use the system, we also provide a [http://theseed.uchicago.edu/FIG/index.cgi public SEED]. The [[Glossary#annotation|annotation]] is performed not on a gene by gene basis per genome, but rather by [[Glossary#subsystem|subsystem]] by an expert curator across many genomes at a time. * You can download software and data from our [[Download]] page. * We provide a list [[Glossary]] of terms used. * When using the SEED, please cite: Overbeek et al., [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16214803&query_hl=2&itool=pubmed_docsum|Nucleic Acids Res 33(17)], 2005 * Ross Overbeek laid out the [[Annotating_1000_genomes|strategy]] for the annotation of the first 1000 genomes. * Our approaches to annotation, gene calling etc are outlined in a series of [[SOPs|Standard Operating Procedures]]. 24607cb547ccfcae76883603439ea80d61571c99 1397 1396 2006-08-11T17:30:45Z FolkerMeyer 2 wikitext text/x-wiki == '''Home of the SEED''' == With the growing number of genomes becoming available, a software environment is needed to produce accurate and consistent annotations. The SEED is that environment, we provide a public [http://explorer.theseed.org/FIG/index.cgi SEED-Viewer] that allows read-only access to the latest data and annotations. For users interested in editing and learning how to use the system, we also provide a [http://theseed.uchicago.edu/FIG/index.cgi public SEED]. The [[Glossary#annotation|annotation]] is performed not on a gene by gene basis per genome, but rather by [[Glossary#subsystem|subsystem]] by an expert curator across many genomes at a time. * You can download software and data from our [[Download]] page. * We provide a list [[Glossary]] of terms used. * When using the SEED, please cite: Overbeek et al., [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16214803&query_hl=2&itool=pubmed_docsum|Nucleic Acids Res 33(17)], 2005 * Ross Overbeek laid out the [[Annotating_1000_genomes|strategy]] for the annotation of the first 1000 genomes. * Our approaches to annotation, gene calling etc are outlined in a series of [[SOPs|Standard Operating Procedures]]. 8322f2b3c7c66f7e77fda467362dd90d58a548bf 1401 1397 2006-08-11T17:32:38Z FolkerMeyer 2 wikitext text/x-wiki == '''Home of the SEED''' == With the growing number of genomes becoming available, a software environment is needed to produce accurate and consistent annotations. The SEED is that environment, we provide a public [http://explorer.theseed.org/FIG/index.cgi SEED-Viewer] that allows read-only access to the latest data and annotations. For users interested in editing and learning how to use the system, we also provide a [http://theseed.uchicago.edu/FIG/index.cgi public SEED]. The [[Glossary#annotation|annotation]] is performed not on a gene by gene basis per genome, but rather by [[Glossary#subsystem|subsystem]] by an expert curator across many genomes at a time. * You can download software and data from our [[DownloadPage]] page. * We provide a list [[Glossary]] of terms used. * When using the SEED, please cite: Overbeek et al., [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16214803&query_hl=2&itool=pubmed_docsum|Nucleic Acids Res 33(17)], 2005 * Ross Overbeek laid out the [[Annotating_1000_genomes|strategy]] for the annotation of the first 1000 genomes. * Our approaches to annotation, gene calling etc are outlined in a series of [[SOPs|Standard Operating Procedures]]. 0ec34b3b3240a3bdbf0384b3c01f3cf6c384b282 1407 1401 2006-08-11T17:42:57Z FolkerMeyer 2 wikitext text/x-wiki == '''Home of the SEED''' == With the growing number of genomes becoming available, a software environment is needed to produce accurate and consistent annotations. The SEED is that environment, we provide a public [http://explorer.theseed.org/FIG/index.cgi SEED-Viewer] that allows read-only access to the latest data and annotations. For users interested in editing and learning how to use the system, we also provide a [http://theseed.uchicago.edu/FIG/index.cgi Trial-SEED]. The [[Glossary#annotation|annotation]] is performed not on a gene by gene basis per genome, but rather by [[Glossary#subsystem|subsystem]] by an expert curator across many genomes at a time. * You can download software and data from our [[DownloadPage]] page. * We provide a list [[Glossary]] of terms used. * When using the SEED, please cite: Overbeek et al., [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16214803&query_hl=2&itool=pubmed_docsum|Nucleic Acids Res 33(17)], 2005 * Ross Overbeek laid out the [[Annotating_1000_genomes|strategy]] for the annotation of the first 1000 genomes. * Our approaches to annotation, gene calling etc are outlined in a series of [[SOPs|Standard Operating Procedures]]. 982961fb1e767b6e19edf6cb47e6581dc98bb521 1408 1407 2006-08-11T17:44:47Z FolkerMeyer 2 [[Main Page]] moved to [[Home of the SEED]]: Home of the SEED wikitext text/x-wiki == '''Home of the SEED''' == With the growing number of genomes becoming available, a software environment is needed to produce accurate and consistent annotations. The SEED is that environment, we provide a public [http://explorer.theseed.org/FIG/index.cgi SEED-Viewer] that allows read-only access to the latest data and annotations. For users interested in editing and learning how to use the system, we also provide a [http://theseed.uchicago.edu/FIG/index.cgi Trial-SEED]. The [[Glossary#annotation|annotation]] is performed not on a gene by gene basis per genome, but rather by [[Glossary#subsystem|subsystem]] by an expert curator across many genomes at a time. * You can download software and data from our [[DownloadPage]] page. * We provide a list [[Glossary]] of terms used. * When using the SEED, please cite: Overbeek et al., [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16214803&query_hl=2&itool=pubmed_docsum|Nucleic Acids Res 33(17)], 2005 * Ross Overbeek laid out the [[Annotating_1000_genomes|strategy]] for the annotation of the first 1000 genomes. * Our approaches to annotation, gene calling etc are outlined in a series of [[SOPs|Standard Operating Procedures]]. 982961fb1e767b6e19edf6cb47e6581dc98bb521 1411 1408 2006-08-11T17:45:59Z FolkerMeyer 2 wikitext text/x-wiki With the growing number of genomes becoming available, a software environment is needed to produce accurate and consistent annotations. The SEED is that environment, we provide a public [http://explorer.theseed.org/FIG/index.cgi SEED-Viewer] that allows read-only access to the latest data and annotations. For users interested in editing and learning how to use the system, we also provide a [http://theseed.uchicago.edu/FIG/index.cgi Trial-SEED]. The [[Glossary#annotation|annotation]] is performed not on a gene by gene basis per genome, but rather by [[Glossary#subsystem|subsystem]] by an expert curator across many genomes at a time. * You can download software and data from our [[DownloadPage]] page. * We provide a list [[Glossary]] of terms used. * When using the SEED, please cite: Overbeek et al., [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16214803&query_hl=2&itool=pubmed_docsum|Nucleic Acids Res 33(17)], 2005 * Ross Overbeek laid out the [[Annotating_1000_genomes|strategy]] for the annotation of the first 1000 genomes. * Our approaches to annotation, gene calling etc are outlined in a series of [[SOPs|Standard Operating Procedures]]. 34b85c7b1c96394f797ec99d3d6cebce43aaf19f 8 1090 1090 2006-07-31T18:04:49Z MediaWiki default 0 wikitext text/x-wiki * navigation ** mainpage|mainpage ** portal-url|portal ** currentevents-url|currentevents ** recentchanges-url|recentchanges ** randompage-url|randompage ** helppage|help ** sitesupport-url|sitesupport af994abf1e4155349addb7f6e4b390a529f7606d 1390 1090 2006-08-11T17:19:46Z FolkerMeyer 2 wikitext text/x-wiki * navigation ** mainpage|Home of the SEED ** downloads|SEED Downloads ** currentevents-url|currentevents ** recentchanges-url|recentchanges ** randompage-url|randompage ** helppage|help ** sitesupport-url|sitesupport c915fbb71842bd41cfc9c7eb7a8d15505d05f017 1391 1390 2006-08-11T17:20:37Z FolkerMeyer 2 wikitext text/x-wiki * navigation ** mainpage|Home of the SEED ** downloads|SEED Download ** currentevents-url|currentevents ** recentchanges-url|recentchanges ** randompage-url|randompage ** helppage|help ** sitesupport-url|sitesupport 19b7ba5d0383265b458ce11b0bcd28af9dbc7bbf 1392 1391 2006-08-11T17:21:25Z FolkerMeyer 2 wikitext text/x-wiki * navigation ** mainpage|Home of the SEED ** Download|SEED Download ** currentevents-url|currentevents ** recentchanges-url|recentchanges ** randompage-url|randompage ** helppage|help ** sitesupport-url|sitesupport 8ebdd23d8c56115c77845fdec47f58549be8a862 1393 1392 2006-08-11T17:23:22Z FolkerMeyer 2 wikitext text/x-wiki * navigation ** mainpage|Home of the SEED ** Download|SEED Download ** Glossary|Glossary 40c9bd654ca19c6871647c2337f5332498f374e5 1394 1393 2006-08-11T17:25:36Z FolkerMeyer 2 wikitext text/x-wiki * navigation ** mainpage|Home of the SEED ** Download|Software and Data Download Page ** Glossary|Glossary 5447726be218102ce39b177dff93d4dd9ecd9e3c 1400 1394 2006-08-11T17:32:25Z FolkerMeyer 2 wikitext text/x-wiki * navigation ** mainpage|Home of the SEED ** DownloadPage|Software and Data Download Page ** Glossary|Glossary c688e7024a2e9e16874d3b8d5e398926c63a2253 1402 1400 2006-08-11T17:33:33Z FolkerMeyer 2 wikitext text/x-wiki * navigation ** mainpage|Home of the SEED ** Annotating_1000_genomes|Manifesto ** DownloadPage|Software and Data Download Page ** Glossary|Glossary a4cd4b47673d94a7b9b6a73a22139107434e15ea 1403 1402 2006-08-11T17:37:05Z FolkerMeyer 2 wikitext text/x-wiki * navigation ** mainpage|Home of the SEED ** Annotating_1000_genomes|Manifesto ** SEEDs *** [http://explorer.theseed.org/FIG/index.cgi|SEED-Viewer] *** [http://theseed.uchicago.edu|public-SEED] ** DownloadPage|Software and Data Download Page ** Glossary|Glossary 1195c45a2285bdd8a055f0fc33237fa81f0a3be1 1404 1403 2006-08-11T17:37:37Z FolkerMeyer 2 wikitext text/x-wiki * navigation ** mainpage|Home of the SEED ** Annotating_1000_genomes|Manifesto ** SEEDs *** http://explorer.theseed.org/FIG/index.cgi SEED-Viewer *** http://theseed.uchicago.edu public-SEED ** DownloadPage|Software and Data Download Page ** Glossary|Glossary 3184553523014779e5a1b092e0e564836f56210b 1405 1404 2006-08-11T17:38:03Z FolkerMeyer 2 wikitext text/x-wiki * navigation ** mainpage|Home of the SEED ** Annotating_1000_genomes|Manifesto ** SEEDs *** http://explorer.theseed.org/FIG/index.cgi|SEED-Viewer *** http://theseed.uchicgo.edu|public-SEED ** DownloadPage|Software and Data Download Page ** Glossary|Glossary c838a733195b4f6c36e00167b94c4d8a3915a02b 1406 1405 2006-08-11T17:41:27Z FolkerMeyer 2 wikitext text/x-wiki * navigation ** mainpage|Home of the SEED ** Annotating_1000_genomes|Manifesto * SEEDs ** http://explorer.theseed.org/FIG/index.cgi|SEED-Viewer ** http://theseed.uchicgo.edu|Trial-SEED * Help and other stuff ** DownloadPage|Software and Data Download Page ** Glossary|Glossary 16829e55484c32d13a1dec59846e3b5a088384db 1410 1406 2006-08-11T17:45:13Z FolkerMeyer 2 wikitext text/x-wiki * navigation ** Home_of_the_SEED|Home of the SEED ** Annotating_1000_genomes|Manifesto * SEEDs ** http://explorer.theseed.org/FIG/index.cgi|SEED-Viewer ** http://theseed.uchicgo.edu|Trial-SEED * Help and other stuff ** DownloadPage|Software and Data Download Page ** Glossary|Glossary 51df8468f91d10c1cbfb7c8cb03bf96fb777e3bf 0 1367 1369 2006-08-01T15:00:24Z FolkerMeyer 2 wikitext text/x-wiki == SEED Glossary == === subsystem === == functional role === e722ddfa0dbba0edf0eac88763500b39a5ff83ca 1370 1369 2006-08-01T15:00:33Z FolkerMeyer 2 wikitext text/x-wiki == SEED Glossary == === subsystem === === functional role === 9f26d055399fb310241af939ff9f59dc8b9883dd 1371 1370 2006-08-01T15:04:33Z FolkerMeyer 2 wikitext text/x-wiki === Annotators SEED === The master copy for all data in the SEED environment. Users can not access this password protected site. === functional role === === peg === A Protein Encoding Gene (PEG) is equivalent to a CDS (Coding Sequence). === subsystem === === subsystem clearing house === 60a6d98608e0d2580bd7825adfc4a97426fef36f 1383 1371 2006-08-01T19:49:07Z 140.221.34.106 0 wikitext text/x-wiki === Annotators SEED === The master copy for all data in the SEED environment. Users can not access this password protected site. === functional role === === peg === A Protein Encoding Gene (PEG) is equivalent to a CDS (Coding Sequence). === subsystem === === subsystem clearing house === ===SEED etyomology=== 0b010e1af5eaf8d07ede70ccccbfa5d0769f8ff0 1384 1383 2006-08-01T19:49:38Z 140.221.34.106 0 wikitext text/x-wiki === Annotators SEED === The master copy for all data in the SEED environment. Users can not access this password protected site. === functional role === === peg === A Protein Encoding Gene (PEG) is equivalent to a CDS (Coding Sequence). === subsystem === === subsystem clearing house === ===SEED etymology=== 32b3caff6803a6514e9462a6041e1a9a1d4a32c6 1385 1384 2006-08-01T20:21:02Z FolkerMeyer 2 wikitext text/x-wiki === Annotators SEED === The master copy for all data in the SEED environment. Users can not access this password protected site. === Annotation === Annotation can be defined as assigning a gene function to a specific sequence. Traditionally annotation has been performed on a gene by gene basis in each genome separately. The SEED approach is based on the idea to annotate many genomes at a time. The SEED approach to annotation requires subsystems to be created, see [[#Clearinghouse]]. === functional role === === PEG === A Protein Encoding Gene (PEG) is equivalent to a CDS (Coding Sequence). === Subsystem === A subsystem is a set of functional roles that together implement a biological process of form a structural complex. === Subsystem Clearing House === Since annotators can work on any machine (including the public SEED) the way to propagate subsystems is via [http://anno-2.nmpdr.org/FIG/p2p/ch.cgi Subsystem Clearing House web page]. ===SEED etymology=== d6c519ec1d7a2df65b4c4f0a3fce6fd626525918 1386 1385 2006-08-01T20:23:51Z FolkerMeyer 2 wikitext text/x-wiki === Annotators SEED === The master copy for all data in the SEED environment. Users can not access this password protected site. === Annotation === Annotation can be defined as assigning a gene function to a specific sequence. Traditionally annotation has been performed on a gene by gene basis in each genome separately. The SEED approach is based on the idea to annotate many genomes at a time. The SEED approach to annotation requires subsystems to be created, see [[#Clearinghouse]]. === Functional role === === PEG === A Protein Encoding Gene (PEG) is equivalent to a CDS (Coding Sequence). === Subsystem === A subsystem is a set of functional roles that together implement a biological process of form a structural complex. === Subsystem Clearing House === Since annotators can work on any machine (including the public SEED) the way to propagate subsystems is via [http://anno-2.nmpdr.org/FIG/p2p/ch.cgi Subsystem Clearing House web page]. ===SEED etymology=== 824242c16ce5e75f609d4d4a3b47ba7d3d8848e7 0 1368 1373 2006-08-01T15:11:59Z FolkerMeyer 2 wikitext text/x-wiki == This is the main SEED download page. == All tools and datasets that make up the SEED are in the public domain and can be downloaded. * SEED code from ADD_URL_HERE ** Source code only ** Binaries for Linux/Intel ** Binaries for Linux/PPC ** Binaries for MacOS/X (universal binaries) * SEED data ** * Subsystem data ** Via the Subsystem Clearing house. * Genomes ** All genomes in GFF3 format 73b0476761f2f5616c55d708f439aa177bbc2f8a 1374 1373 2006-08-01T15:16:41Z FolkerMeyer 2 wikitext text/x-wiki == This is the main SEED download page. == All tools and datasets that make up the SEED are in the public domain and can be downloaded. * SEED code from ftp://ftp.theseed.org ** Source code only ** Binaries for Linux/Intel ** Binaries for Linux/PPC ** Binaries for MacOS/X (universal binaries) * SEED data ** * Subsystem data ** Via the Subsystem Clearing house. * Genomes ** All genomes in GFF3 format b974a17d1c257bf893fa2380da83dcdb89b005e0 1375 1374 2006-08-01T15:18:58Z FolkerMeyer 2 wikitext text/x-wiki == This is the main SEED download page. == All tools and datasets that make up the SEED are in the public domain and can be downloaded. * SEED code via ftp://ftp.theseed.org ** Source code only ** Binaries for Linux/Intel ** Binaries for Linux/PPC ** Binaries for MacOS/X (universal binaries) * SEED data via ftp://ftp.theseed.org ** * Subsystem data ** Via the Subsystem Clearing house. * Genomes via ftp://ftp.theseed.org ** All genomes in GFF3 format 69df84949699f522f25af34eede52f4307a425f2 1395 1375 2006-08-11T17:28:05Z FolkerMeyer 2 wikitext text/x-wiki == This is the main SEED download page. == All tools and datasets that make up the SEED are in the public domain and can be downloaded. * SEED code via ftp://ftp.theseed.org ** Source code only ** Binaries for Linux/Intel ** Binaries for Linux/PPC ** Binaries for MacOS/X (universal binaries) * SEED data via ftp://ftp.theseed.org ** * Subsystem data ** Via the [http://clearinghouse.theseed.org/clearinghouse_browser.cgi?|Subsystem Clearing house]. * Genomes via ftp://ftp.theseed.org ** All genomes in GFF3 format 802ace5e3ad378d878a0045f0b6e61c7ad8e83d4 1398 1395 2006-08-11T17:31:50Z FolkerMeyer 2 [[Download]] moved to [[DownloadPage]]: download wikitext text/x-wiki == This is the main SEED download page. == All tools and datasets that make up the SEED are in the public domain and can be downloaded. * SEED code via ftp://ftp.theseed.org ** Source code only ** Binaries for Linux/Intel ** Binaries for Linux/PPC ** Binaries for MacOS/X (universal binaries) * SEED data via ftp://ftp.theseed.org ** * Subsystem data ** Via the [http://clearinghouse.theseed.org/clearinghouse_browser.cgi?|Subsystem Clearing house]. * Genomes via ftp://ftp.theseed.org ** All genomes in GFF3 format 802ace5e3ad378d878a0045f0b6e61c7ad8e83d4 0 1369 1381 2006-08-01T15:41:48Z FolkerMeyer 2 wikitext text/x-wiki The Project to Annotate the First 1000 Sequenced Genomes, Develop Detailed Metabolic Reconstructions, and Construct the Corresponding Stoichiometric Matrices by Ross Overbeek === Introduction === In December, 2003 The Fellowship for Interpretation of Genomes (FIG) initiated The Project to Annotate 1000 Genomes. The explicit goal was to develop a technology for more accurate, high-volume annotation of genomes and to use this technology to provide superior annotations for the first 1000 sequenced genomes. Members of FIG were convinced that the current approaches for high-throughput annotation, based on protein families and automated pipelines that processed genomes sequentially, would ultimately fail to produce annotations of the desired accuracy. We believe that the key to development of high-throughput annotation technology is to have experts annotate single subsystems over the complete collection of genomes. The existing annotation approaches, in which teams analyze a whole genome at a time, ensure that annotators have no special expertise relating to the vast majority of genes they annotate. By having individuals annotate single subsystems over a large collection of genomes, we allow individuals with expertise in specific pathways (or, more generally, subsystems) to perform their task with relatively high accuracy. The early stages of the effort began at FIG, but quickly spread to a number of cooperating institutions, most notably Argonne National Lab. During the first year of the project, we have developed detailed encodings of subsystems that include a majority of the genes from subsystems that make up the core cellular machinery. More importantly, we have developed the initial versions of technology needed to support the project. The Project to Annotate 1000 Genomes has reached the stage where it is clear that it will very shortly produce what we call informal metabolic reconstructions that cover the majority of central metabolism as it is implemented in the close to 300 more-or-less complete genomes that are now available. We think of an informal metabolic reconstruction as a partitioning of the cellular machinery into subsystems, the specification of the functional roles that make up each subsystem, and the inventory of which genes in a specific organism implement the functional roles. What is needed to support both qualitative analysis and effective quantitative modeling is to convert these informal metabolic reconstructions into formal metabolic reconstructions. By a formal reconstruction, we mean an accurate encoding of the metabolic network. The goal of such an encoding is to construct a list of metabolites and a detailed reaction network that is internally consistent (in the sense that metabolites that are produced by reactions are connected as substrates to other reactions or to specific transporters, and that all metabolites that act as substrates are produced by other reactions or provided by transporters). Perhaps, a better way to put this is that all apparent anomalies are highlighted as such, and the essential components of the metabolic network are accurately encoded. The output of such an effort is normally what is termed a stoichiometric matrix, the basic resource required to support stoichiometric modeling. One of the central goals of this enlarged effort is to develop accurate stoichiometric matrices for each of the 1000 genomes; we refer to this component of the effort as The Project to Produce 1000 Stoichiometric Matrices. It is our belief that the development of the technology required to mass-produce accurate genome annotations will ultimately allow fully automated annotation pipelines to achieve relatively high accuracy. Similarly, the existence of 1000 accurate formal metabolic reconstructions would constitute a resource that would allow rapid and accurate development of stoichiometric matrices for newly-sequenced genomes. That is, besides producing accurate annotations, informal metabolic reconstructions, formal metabolic reconstructions, and stoichiometric matrices for a large collection of diverse genomes, we believe that the expanded project will produce technology that will support nearly automatic, very rapid characterization of new genomes. All of the encoded subsystems, metabolic reconstructions and stoichiometric matrices will be made freely available on open web sites. In addition, the software environments used to develop the encoded subsystems and stoichiometric matrices will be developed and supported as open source software. By making the fundamental data items, the encoded subsystems and stoichiometric matrices, freely available to the community, we expect to stimulate development of alternative software systems to support curation and maintenance of these items. === The Project to Annotate 1000 Genomes === We have chosen to conceptually break the Project to Annotate 1000 Genomes into three stages. We discuss these stages as if they will occur sequentially; in fact, all three stages are now in progress. To understand the three stages, the reader must have at least a rudimentary grasp of what we mean by an encoded subsystem and an informal metabolic reconstruction. When we speak of a subsystem, we think of a set of related functional roles. In a specific organism, a set of genes implement these roles, and we think of those genes as constituting the subsystem in that organism. That is, we are really dealing with an abstract notion of subsystem (in which the subsystem is a set of functional roles) and instances of the subsystem in a specific organism (in which a set of genes implements the abstract functional roles). Precisely the same subsystem and functional roles exist in distinct organisms, although obviously the genes are unique to each organism. Subsystems are thought of as possibly having multiple variants. Organisms that have operational versions of a subsystem may well have genes that implement slightly different subsets of the functional roles that make up the subsystem. Each subset of functional roles that exists in at least one organism with an operational version of the subsystem constitutes an operational variant. We think of an informal metabolic reconstruction for an organism as a set of operational variants of subsystems that are believed to exist for the organism. In this conceptualization, one does not have a meaningful functional hierarchy or DAG; rather, we simply have an inventory of functional roles that are implemented in the organism, along with the variants of subsystems that they implement. We do believe that the task of imposing an actual hierarchy is relatively straightforward in comparison with the effort required to construct the set of operational variants. In some contexts, we have included a functional overview in which the subsystems are embedded at the lowest levels. It is clear that, given a diverse collection of informal metabolic reconstructions, the development of appropriate functional hierarchies can be generated with relatively few resources. Our encoding of a subsystem can now be reduced to a specification of a set of functional roles (this amounts to the abstract subsystem) and sets of genes which implement the operational variants in a number of genomes. These genes are given as a subsystem spreadsheet in which each row corresponds to a single genome, each column corresponds to a single functional role, and each cell contains the set of genes in that genome that are believed to implement the given functional role. The Project to Annotate 1000 Genomes amounts to an effort to produce detailed and comprehensive encodings of several hundred subsystems, which will impose assigned functions on genes in each of the genomes. The total percent of genes that can be assigned functions this way is probably on the order of 50-70% in most genomes (in large eukaryotic genomes the total is obviously substantially lower). The percent will grow as our understanding grows. What should be noted is that the accuracy of these assignments will be substantially better than that of current assignments, and the conserved cellular machinery almost all falls within the projected subsystems. Once we have produced our initial set of annotations, we believe that automated pipelines and protein families are excellent tools for propagating them. Protein families are, in fact, a key component of annotation and provide the fundamental mechanism for projection of function between genes. The added dimension provided by subsystems, along with the manual curation required to develop accurate initial encodings of subsystems, is an essential technology for increasing the accuracy and effectiveness of protein families. Ultimately the encoded subsystems will be used to make incremental, essential corrections to collections of protein families (like those supported by UniProt and COGs), and a basis for much more accurate annotation will emerge. === We now proceed to describe the details of the three stages. === ==== Stage 1: Development of Initial Encodings of Subsystems ==== The initial stage of the project will involve development of approximately 100-150 subsystems that will cover most of the conserved cellular machinery in prokaryotes (and all of the central metabolic machinery in eukaryotes). This work will be done largely by trained annotators who achieve a limited mastery of specific subsystems via review articles and detailed analysis of the collection of genomes. These individuals can define the abstract subsystems and add most genomes to the emerging spreadsheets, but not without error. They are necessarily far less skilled than experts who have invested tens of years in study of specific subsystems. These initial subsystems will have many uses. They can be used to enhance sets of curated protein families, to clarify identification of gene starts, and to develop a consistent set of annotations. They will form the basis of informal metabolic reconstructions, and will be used to support the development of formal metabolic reconstructions. However, given the relative lack of expertise of these initial annotators and the fact that they will seldom have access to the wet lab facilities needed to remove ambiguities in assignments, errors will inevitably remain. ==== Stage 2: The Use of True Experts and the Wet Lab to Refine the Encodings ==== The second stage will involve the gradual refinement and enhancement of the original subsystem encodings by domain experts. Almost every subsystem spreadsheet makes it clear that numerous detailed questions remain to be answered. These questions relate to correcting gene calls, correction of frameshifts, refining function assignments, and removing ambiguities (either via bioinformatics based analysis or through actual wet lab efforts). The participation of domain experts will be critical, but it seems most likely that a relatively small set will choose to get involved until the utility of the approach becomes obvious. We already have some domain experts (in translation, transcription, and a limited number of metabolic subsystems) participating in the effort. We believe that this number will grow rapidly over the next 2-3 years. It should be emphasized that upon completion of step 2 we will have accurate annotations and a solid foundation for the construction of stoichiometric matrices. ==== Stage 3: Understanding the Evolutionary History of the Genes within the Subsystem ==== The third stage involves determination of the evolutionary history of the genes within the subsystem. To understand what this involves and the utility of this type of analysis, we must simply recommend two papers by the team led by Roy Jensen: Ancient origin of the tryptophan operon and the dynamics of evolutionary change by Xie, Keyhani, Bonner, Jensen, Microbiol Mol Biol Rev. 2003 Sep;67(3):303-42 Inter-genomic displacement via lateral transfer of bacterial trp operons in an overall context of vertical genealogy, by Xie, Song, Keyhani, Bonner, Jensen, BMC Biology, 2004, 2:15 These papers elegantly display the exact style of analysis required to uncover and clarify the evolutionary history of the relevant genes. Essentially, trees must be built containing all of the genes implementing each specific functional role (multiple trees may be needed for distinct forms). Those trees that display a common topology indicate which columns in the spreadsheet can be used to infer the most probable vertical history of the subsystem. Once the overall history has been clarified, it becomes possible to attempt clarification of horizontal transfers, to reconstruct the history of clusters on the chromosome, and in some cases to tie the analysis to regulatory issues. The effort required to do this style of analysis well is high. While we expect the initial efforts to go slowly, we also expect experience and advances in tools to dramatically reduce the required effort. In any event, it is clear that this stage will not be completed in the next few years, but will undoubtedly stimulate large amounts of related research. === Filling in the Missing Pieces === The encoded subsystems produced by the Project to Annotate 1000 Genomes offer a detailed picture of exactly what components have been identified and are present in each genome. Perhaps as significant, they vividly display exactly what is missing or ambiguous, allowing one to arrive at an accurate inventory of gaps in our understanding. The issue of how best to address these gaps is an integral part of the project. The technology that is emerging is what we refer to as the bioinformatics-driven wet lab. This concept refers to the development of a wet lab that utilizes conventional biochemical and genetic techniques in a framework designed to maximize the overall number of confirmations. It is driven by predictions arising from the analysis of subsystems, and it targets a prioritized list of conjectures. That is, the explicit goal is to fill in as many gaps and remove as many ambiguities as possible for resources consumed. Although it is inconceivable that one experimental group would be able to assess all of the functional predictions, we believe that integrating an experimental component into our annotation/modeling effort will directly support our main goal. In addition to verification of key predictions and removal of central ambiguities, it will validate the overall approach and set an example for other groups worldwide. === The Project to Develop 1000 Stoichiometric Matrices === We believe that the informal metabolic reconstructions are of substantial value by themselves. Indeed, numerous applications are quite obvious. However, they are not enough to support quantitative modeling. Whole genome modeling will require development of stoichiometric matrices, an effort that will pay many dividends. The most immediate payout is as quality control on the informal metabolic reconstruction. Just as the use of subsystems imposes a critical set of consistency checks on the assignment of function to genes, an attempt to develop an internally consistent reaction network imposes a strong consistency check on both the annotations and assertions of the presence of specific subsystems. Over the last 4-5 years, the success of stoichiometric modeling has set the stage for large-scale employment of the technology. The key limiting factor is the development of the stoichiometric matrix itself. This is a time-consuming task that frequently requires on the order of a year for a skilled practitioner. Many actual modeling efforts have foundered on just the technical difficulties in producing this basic datum. Bernhard Palsson has pioneered much of the key research that has led to the recent successes. Spending large amounts of effort, his team has built a very few of these stoichiometric matrices, iteratively improving their accuracy. They have successfully used these matrices to support initial modeling efforts on the organisms, and the results have gained international recognition. Palsson�s team originated the The Project to Produce 1000 Stoichiometric Matrices, and they will play the lead role in converting the informal metabolic reconstructions into formal reconstructions and produce the matrices. The team at FIG and Argonne National Laboratory will participate in the effort, coordinating closely with Palsson�s team. At this point, the Palsson team and the teams at FIG, ANL, and The Burnham Institute are all working on issues relating to tools to automate the generation of matrices from informal metabolic reconstructions. === The Participants === We expect participants in both projects from many institutions worldwide, probably with both academic and commercial interests. Initially, it is likely that the effort will be led from FIG, ANL and Palsson�s team at UCSD. We are planning on Roy Jensen playing a role relating to quality control and development of tools to support Stage 3 analysis. Andrei Osterman from the Burnham Institute will lead wet lab efforts to challenge in silico predictions. If the effort is successful, we would hope to stimulate numerous research efforts worldwide, and we welcome broad participation. Ultimately, leadership and participation will broaden rapidly, if the effort is successful. === A Proposed Schedule === Let us begin by estimating the point at which 1000 genomes will become available. One simple approach would go as follows: The number of genomes will double approximately every 18 months. We now have about 300 more-or-less complete genomes. Therefore, we should have approximately 1000 genomes in just a bit under 3 years (by sometime in 2007) There is a great deal in this analysis that is far from certain. However, let us use this estimate as a working hypothesis. ==== 2005 ==== During 2005, Stage 1 will be completed for the vast majority of subsystems. Stage 2 will be initiated for 30-50 subsystems. Less than 10 will move deeply into stage 3. We will actively attempt to produce 10-15 stoichiometric matrices. We will focus on diverse organisms of interest to DOE and a set of gram-positive pathogens. We will begin a detailed review for quality assurance by a small number of expert biochemists and microbiologists. We expect wet lab confirmations to begin, but this is one area in which funding plays an essential role. We expect funding to support targeted confirmation/rejection of the numerous conjectures arising from the bioinformatics to begin in 2005-2006. It is possible to fairly accurately predict the potential flow of confirmations, but we cannot predict available funding. We believe that the bioinformatics-driven wet lab, in which conjectures are prioritized and grouped, would allow a relatively small group (of 3-4 postdocs and technician) to characterize up to 50 novel gene families encoding the most important functional roles in central metabolic subsystems of diverse organisms per year. ==== 2006 ==== During 2006, the vast majority of subsystems will enter Stage 2. We will attempt to move a large number into Stage 3 (this is truly difficult to predict; it depends hugely on success with the early attempts, our ability to reduce the required effort, and the research aims of the participants). We would plan on completing at least 200 more stoichiometric matrices. If the wet lab component of the effort is fully functional, we would expect a steady stream of confirmations, and (based on our past experience) we would project roughly that 75-90% of the tested conjectures will be validated. ==== 2007 ==== During 2007 we would plan on pushing Stage 2 and 3 analysis as far as possible. We believe that we will have the subsystems needed to cover the vast majority of well understood subsystems and many that are not well understood. We would plan on completing initial stoichiometric matrices for several hundred more genomes. Since the majority of the genomes will not become available until this year, of necessity many of the stoichiometric matrices will not be reasonably complete before sometime in 2008 or 2009. If the wet lab component of the effort is fully functional, we would expect the stream of successful conjectures to stimulate numerous labs to join the effort. Ultimately, the role of the wet lab component that is tightly-coupled to the project is to demonstrate the huge improvement in efficiency that can be attained by coupling the wet lab effort to well-chosen, targeted conjectures generated from the subsystems. === A Short Note on the Analysis of Environmental Samples === It is becoming clear that analysis of environmental samples will become increasingly significant. Consider a framework in which we have 1000 genomes and detailed informal metabolic reconstructions for all of them. We believe that, given a substantial environmental sample, it will be possible to produce accurate estimates of which organisms are present (where an "organism" in this context should probably be viewed as "some organism within a very constrained phylogenetic neighborhood"), it will be possible to produce fairly precise estimates of the metabolism of the organisms believed to be present, and it will be possible to compared the predicted metabolism with the actual enzymes detected in the environmental sample. The hope is clearly that we will be able to make accurate estimates, given 1000 well-annotated genomes. == Summary == The value of a collection of 1000 genomes depends directly on the quality of the annotations, the corresponding metabolic reconstructions, and the extent to which the foundations of modeling have been established. The Project to Annotate 1000 Genomes is based directly on the notion of building a collection of carefully created and curated subsystems. The fact that the individuals who encode these subsystems annotate the same subsystem over a broad collection of genomes allows them to gain an understanding of detailed variation and at least a minimal grasp of the review literature. They will be annotating genes for which they develop some detailed familiarity. We place this technology in direct opposition to the existing approaches in which individuals annotate complete genomes (assuring an almost complete lack of familiarity with the majority of genes being annotated), and automated pipelines are badly limited by the ambiguities and errors in existing annotations. The Project to Produce 1000 Stoichiometric Matrices has the potential of laying the foundations for quantitative modeling. Many, if not most, existing modeling efforts are dramatically hampered by the fact that very, very few stoichiometric matrices now exist, and the cost of developing more using existing approaches is quite high. The development of a wet lab component that challenges a carefully prioritized set of conjectures flowing from both the subsystems analysis and the initial modeling based on quantitative modeling is essential. It will confirm the relative efficiency of this approach (which might reasonably be characterized as "picking the low-hanging fruit"), and in the process establish a paradigm that directly challenges the more common approach to establishing priorities. We claim to understand the key technology needed to develop high-throughput development of annotations, metabolic reconstructions, and stoichiometric matrices. By the summer of 2005, this should be completely obvious. c740087f27c4ba52bb317cd341f66660de32a2ec 6 1370 1382 2006-08-01T19:01:45Z WikiSysop 1 wikitext text/x-wiki da39a3ee5e6b4b0d3255bfef95601890afd80709 0 1371 1388 2006-08-01T20:27:48Z FolkerMeyer 2 wikitext text/x-wiki == SEED standard operating procedures == To generate data that is usefull to the various communities involved in the process of annotation and use of annotations, we make available out standard operating procedures. * Gene calling ** Gene calling for close strain sets ** Gene calling for diverse prokaryotes ** Gene calling for Eukayotes * Annotation ** Annotation of close strain sets ** Annotation of diverse genomes. c68b43e32fd81d7a90a69a647ed8e00ab712b04f 0 1372 1399 2006-08-11T17:31:50Z FolkerMeyer 2 [[Download]] moved to [[DownloadPage]]: download wikitext text/x-wiki #REDIRECT [[DownloadPage]] 26d31e3d8bcda3dc505e26a393f3a713b260b679 0 1373 1409 2006-08-11T17:44:47Z FolkerMeyer 2 [[Main Page]] moved to [[Home of the SEED]]: Home of the SEED wikitext text/x-wiki #REDIRECT [[Home of the SEED]] 7b121fdcffbfb09d10111c17b26b45c99989ee4f 0 1374 1412 2006-08-11T17:50:28Z FolkerMeyer 2 wikitext text/x-wiki The people behind SEED are the following: * [http://www.thefig.info/|FIG] ** * [http://www.mcs.anl.gov|Mathematics and Computer Science Department|Argonne National Labs] ** * [http://www.ci.uchicago.edu| Computation Institure, University of Chicago] ** 75c5b733badcb2c53001bc3b33659c474664891a 1413 1412 2006-08-11T17:50:55Z FolkerMeyer 2 wikitext text/x-wiki The people behind SEED are the following: * [http://www.thefig.info|FIG] ** * [http://www.mcs.anl.gov|Mathematics and Computer Science Department|Argonne National Labs] ** * [http://www.ci.uchicago.edu| Computation Institure, University of Chicago] ** 256db400cd8845a350bb031f04b6e41caa49814d 1414 1413 2006-08-11T17:51:18Z FolkerMeyer 2 wikitext text/x-wiki The people behind SEED are the following: * [http://www.thefig.info |FIG] ** * [http://www.mcs.anl.gov|Mathematics and Computer Science Department|Argonne National Labs] ** * [http://www.ci.uchicago.edu| Computation Institure, University of Chicago] ** 0db7c7356c2c82e79ed5259646c221d94c80a4bc 0 1374 1415 1414 2006-08-11T17:51:29Z FolkerMeyer 2 wikitext text/x-wiki The people behind SEED are the following: * [http://www.thefig.info FIG] ** * [http://www.mcs.anl.gov|Mathematics and Computer Science Department|Argonne National Labs] ** * [http://www.ci.uchicago.edu| Computation Institure, University of Chicago] ** 6c2954e85a10a4d1c80d8fa852099311ed97a763 1416 1415 2006-08-11T17:51:50Z FolkerMeyer 2 wikitext text/x-wiki The people behind SEED are the following: * [http://www.thefig.info FIG] ** * [http://www.mcs.anl.gov Mathematics and Computer Science Department|Argonne National Labs] ** * [http://www.ci.uchicago.ed Computation Institure, University of Chicago] ** 9a6173b2aec76d04a0ab5066abc0f96ad13e9425 1417 1416 2006-08-11T17:52:20Z FolkerMeyer 2 wikitext text/x-wiki The people behind SEED are the following: * [http://www.thefig.info FIG] ** * [http://www.mcs.anl.gov Mathematics and Computer Science Department] [http://www.anl.gov Argonne National Labs] ** * [http://www.ci.uchicago.ed Computation Institure] [http://www.uchicago.edu University of Chicago] ** 6e6191130b8102f59731faa1c8a03525ca621971 1418 1417 2006-08-11T17:54:09Z FolkerMeyer 2 wikitext text/x-wiki The people behind SEED are the following: * [http://www.thefig.info FIG] ** Ross Overbeek ** Veronika Vonstein ** Gordon Pusch ** Bruce Parello ** Rob Edwards ** Andrei Ostermann ** ... * [http://www.mcs.anl.gov Mathematics and Computer Science Department] [http://www.anl.gov Argonne National Labs] ** Rick Stevens ** Terry Disz ** Robert Olson ** Kaitlyn Hwang ** Folker Meyer ** ... * [http://www.ci.uchicago.ed Computation Institure] [http://www.uchicago.edu University of Chicago] ** Michael Kubal ** Daniela Bartels ** Tobias Paczian ** ... d71d57d58f1d3feab81a0c13a74327fd52b4f8b5 1428 1418 2006-08-11T18:24:48Z FolkerMeyer 2 wikitext text/x-wiki The people behind SEED are the following: * [http://www.thefig.info FIG] ** Ross Overbeek ** Veronika Vonstein ** Gordon Pusch ** Bruce Parello ** Rob Edwards ** Andrei Ostermann ** Michael Fonstein ** Svetlana Gerdes ** Olga Zagnitko ** Olga Vassieva ** ... * [http://www.mcs.anl.gov Mathematics and Computer Science Department] [http://www.anl.gov Argonne National Labs] ** Rick Stevens ** Terry Disz ** Robert Olson ** Kaitlyn Hwang ** Folker Meyer ** ... * [http://www.ci.uchicago.ed Computation Institure] [http://www.uchicago.edu University of Chicago] ** Michael Kubal ** Matt Cohoon ** Jen Zinner ** Daniela Bartels ** Tobias Paczian ** ... * [http://www.uiuc.edu University of Illinois at Urbana-Champaign] ** Gary J. Olson ** Leslie McNeil * [http://www.hope-college.edu Hope College] ** Matt DeJongh ** Aaron Best 338e6743f7c8e3653c907e0e0255dbab99674ae4 1429 1428 2006-08-11T18:26:09Z FolkerMeyer 2 wikitext text/x-wiki The people behind SEED are the following: * [http://www.thefig.info FIG] ** Ross Overbeek ** Veronika Vonstein ** Gordon Pusch ** Bruce Parello ** Rob Edwards ** Andrei Ostermann ** Michael Fonstein ** Svetlana Gerdes ** Olga Zagnitko ** Olga Vassieva ** ... * [http://www.mcs.anl.gov Mathematics and Computer Science Department] [http://www.anl.gov Argonne National Labs] ** Rick Stevens ** Terry Disz ** Robert Olson ** Kaitlyn Hwang ** Folker Meyer ** ... * [http://www.ci.uchicago.ed Computation Institure] [http://www.uchicago.edu University of Chicago] ** Michael Kubal ** Matt Cohoon ** Jen Zinner ** Daniela Bartels ** Tobias Paczian ** ... * [http://www.uiuc.edu University of Illinois at Urbana-Champaign] ** Gary J. Olson ** Leslie McNeil * [http://www.hope-college.edu Hope College] ** Matt DeJongh ** Aaron Best * [http://www.utmem.edu/ University of Memphis Tennessee] ** Rami Aziz 6b950a15baff36063860c6fd7ee813971775b3d0 1430 1429 2006-08-11T18:40:25Z WilliamMihalo 3 wikitext text/x-wiki The people behind SEED are the following: * [http://www.thefig.info FIG] ** Ross Overbeek ** Veronika Vonstein ** Gordon Pusch ** Bruce Parello ** Rob Edwards ** Andrei Ostermann ** Michael Fonstein ** Svetlana Gerdes ** Olga Zagnitko ** Olga Vassieva ** ... * [http://www.mcs.anl.gov Mathematics and Computer Science Department] [http://www.anl.gov Argonne National Labs] ** Rick Stevens ** Terry Disz ** Robert Olson ** Kaitlyn Hwang ** Folker Meyer ** ... * [http://www.ci.uchicago.ed Computation Institure] [http://www.uchicago.edu University of Chicago] ** Michael Kubal ** Matt Cohoon ** Jen Zinner ** Daniela Bartels ** Tobias Paczian ** William Mihalo ** ... * [http://www.uiuc.edu University of Illinois at Urbana-Champaign] ** Gary J. Olson ** Leslie McNeil * [http://www.hope-college.edu Hope College] ** Matt DeJongh ** Aaron Best * [http://www.utmem.edu/ University of Memphis Tennessee] ** Rami Aziz 9c82cc413aa7410f111be80497989819bd1e953b 1437 1430 2006-08-13T15:01:17Z FolkerMeyer 2 wikitext text/x-wiki The people behind SEED are the following: * [http://www.thefig.info FIG] ** Ross Overbeek ** Veronika Vonstein ** Gordon Pusch ** Bruce Parello ** Rob Edwards ** Andrei Ostermann ** Michael Fonstein ** Svetlana Gerdes ** Olga Zagnitko ** Olga Vassieva ** ... * [http://www.mcs.anl.gov Mathematics and Computer Science Department] [http://www.anl.gov Argonne National Labs] ** Rick Stevens ** Terry Disz ** Robert Olson ** Kaitlyn Hwang ** Folker Meyer ** ... * [http://www.ci.uchicago.ed Computation Institure] [http://www.uchicago.edu University of Chicago] ** Michael Kubal ** Matt Cohoon ** Jen Zinner ** Daniela Bartels ** Tobias Paczian ** Andreas Wilke ** Daniel Paarmann ** William Mihalo ** ... * [http://www.uiuc.edu University of Illinois at Urbana-Champaign] ** Gary J. Olson ** Leslie McNeil * [http://www.hope-college.edu Hope College] ** Matt DeJongh ** Aaron Best * [http://www.utmem.edu/ University of Memphis Tennessee] ** Rami Aziz 5e4f3425e6eec7ac892a58507fe8d74f0dcc4071 8 1090 1419 1410 2006-08-11T17:54:37Z FolkerMeyer 2 wikitext text/x-wiki * navigation ** Home_of_the_SEED|Home of the SEED ** Annotating_1000_genomes|Manifesto ** SEED_People| SEED People * SEEDs ** http://explorer.theseed.org/FIG/index.cgi|SEED-Viewer ** http://theseed.uchicgo.edu|Trial-SEED * Help and other stuff ** DownloadPage|Software and Data Download Page ** Glossary|Glossary 1edb3c9c3e46d5909ae21ebb0afa7c0fa38ccaa1 1421 1419 2006-08-11T17:56:11Z FolkerMeyer 2 wikitext text/x-wiki * navigation ** Home_of_the_SEED|Home of the SEED ** Annotating_1000_genomes|Manifesto ** SEED_People| SEED People ** Contact| Contact * SEEDs ** http://explorer.theseed.org/FIG/index.cgi|SEED-Viewer ** http://theseed.uchicgo.edu|Trial-SEED * Help and other stuff ** DownloadPage|Software and Data Download Page ** Glossary|Glossary d06d9157934e1e2f1764b11ccfa7ba9f4b4f55ea 1422 1421 2006-08-11T17:57:00Z FolkerMeyer 2 wikitext text/x-wiki * navigation ** Home_of_the_SEED|Home of the SEED ** Annotating_1000_genomes|Manifesto ** SEED_People| SEED People ** Contact| Contact * SEEDs ** http://explorer.theseed.org/FIG/index.cgi|SEED-Viewer ** http://theseed.uchicgo.edu|Trial-SEED * Help and other stuff ** DownloadPage|Software and Data Download Page ** Glossary|Glossary ** misc|Miscellaneous stuff cc22353700149d53ff8e548af082a855fe5513ae 1431 1422 2006-08-11T18:43:52Z FolkerMeyer 2 wikitext text/x-wiki * navigation ** Home_of_the_SEED|Home of the SEED ** Annotating_1000_genomes|Manifesto ** SEED_People| SEED People ** Contact| Contact * SEEDs ** http://explorer.theseed.org/FIG/index.cgi|SEED-Viewer ** http://theseed.uchicago.edu|Trial-SEED * Help and other stuff ** DownloadPage|Software and Data Download Page ** Glossary|Glossary ** misc|Miscellaneous stuff 37f6a2896eeeb15f51d2357afb588e2edd371368 1432 1431 2006-08-11T18:44:34Z FolkerMeyer 2 wikitext text/x-wiki * navigation ** Home_of_the_SEED|Home of the SEED ** Annotating_1000_genomes|Manifesto ** SEED_People| SEED People ** Contact| Contact * SEEDs ** http://explorer.theseed.org/FIG/index.cgi|SEED-Viewer ** http://theseed.uchicago.edu/FIG/index.cgi|Trial-SEED * Help and other stuff ** DownloadPage|Software and Data Download Page ** Glossary|Glossary ** misc|Miscellaneous stuff 936b346d726006ea6893de8bbcc665792db6c2ac 1438 1432 2006-08-13T15:03:42Z FolkerMeyer 2 wikitext text/x-wiki * navigation ** Home_of_the_SEED|Home of the SEED ** Annotating_1000_genomes|Manifesto ** SEED_People| SEED People ** Contact| Contact * SEEDs ** http://explorer.theseed.org/FIG/index.cgi|SEED-Viewer ** http://theseed.uchicago.edu/FIG/index.cgi|Trial-SEED * Help and other Materials ** DownloadPage|Software and Data Download Page ** Glossary|Glossary ** misc|Miscellaneous Materials b2c75c2a75d5c1efde27766d02cf80a178d4ba33 0 1375 1420 2006-08-11T17:55:33Z FolkerMeyer 2 wikitext text/x-wiki If you want to contact us please use the following email address: SOME ADDRESS HERE af468681ba5cc8f3db81cf0482f580332ff09dd7 0 1376 1423 2006-08-11T17:59:54Z FolkerMeyer 2 wikitext text/x-wiki There are numerous pages with information on the SEED floating around. This page attempts to collect links to them * [http://www-unix.mcs.anl.gov/SEEDWiki/ SEED installation Wiki] * [http://www.theseed.org/SubsystemPaperSupplementalMaterial/index.html| Supplementary material for the NAR Subsystem Paper] 018113e95631f5cdf3e4dd60f0c01d466062ce85 0 1 1424 1411 2006-08-11T18:09:53Z FolkerMeyer 2 wikitext text/x-wiki With the growing number of genomes becoming available, a software environment is needed to produce accurate and consistent annotations. The SEED is that environment. We provide a public [http://explorer.theseed.org/FIG/index.cgi SEED-Viewer] that allows read-only access to the latest data and annotations. For users interested in editing and learning how to use the system, we also provide a [http://theseed.uchicago.edu/FIG/index.cgi Trial-SEED]. As described in our [[Annotating_1000_Genomes|manifesto] the [[Glossary#annotation|annotation]] is not performed on a gene by gene basis per genome, but rather by [[Glossary#subsystem|subsystem]] by an expert curator across many genomes at a time. * You can download software and data from our [[DownloadPage]] page. * We provide a list [[Glossary]] of terms used. * When using the SEED, please cite: Overbeek et al., [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16214803&query_hl=2&itool=pubmed_docsum|Nucleic Acids Res 33(17)], 2005 * Our approaches to annotation, gene calling etc are outlined in a series of [[SOPs|Standard Operating Procedures]]. 77d7b377651c9e4a16520772c6028117becf0cce 1425 1424 2006-08-11T18:10:05Z FolkerMeyer 2 wikitext text/x-wiki With the growing number of genomes becoming available, a software environment is needed to produce accurate and consistent annotations. The SEED is that environment. We provide a public [http://explorer.theseed.org/FIG/index.cgi SEED-Viewer] that allows read-only access to the latest data and annotations. For users interested in editing and learning how to use the system, we also provide a [http://theseed.uchicago.edu/FIG/index.cgi Trial-SEED]. As described in our [[Annotating_1000_Genomes|manifesto]] the [[Glossary#annotation|annotation]] is not performed on a gene by gene basis per genome, but rather by [[Glossary#subsystem|subsystem]] by an expert curator across many genomes at a time. * You can download software and data from our [[DownloadPage]] page. * We provide a list [[Glossary]] of terms used. * When using the SEED, please cite: Overbeek et al., [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16214803&query_hl=2&itool=pubmed_docsum|Nucleic Acids Res 33(17)], 2005 * Our approaches to annotation, gene calling etc are outlined in a series of [[SOPs|Standard Operating Procedures]]. 4bafea0f5e859e40a75ba7e10a045d3a16f50b12 1426 1425 2006-08-11T18:10:44Z FolkerMeyer 2 wikitext text/x-wiki With the growing number of genomes becoming available, a software environment is needed to produce accurate and consistent annotations. The SEED is that environment. We provide a public [http://explorer.theseed.org/FIG/index.cgi SEED-Viewer] that allows read-only access to the latest data and annotations. For users interested in editing and learning how to use the system, we also provide a [http://theseed.uchicago.edu/FIG/index.cgi Trial-SEED]. As described in our [[Annotating_1000_genomes|manifesto]] the [[Glossary#annotation|annotation]] is not performed on a gene by gene basis per genome, but rather by [[Glossary#subsystem|subsystem]] by an expert curator across many genomes at a time. * You can download software and data from our [[DownloadPage]] page. * We provide a list [[Glossary]] of terms used. * When using the SEED, please cite: Overbeek et al., [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16214803&query_hl=2&itool=pubmed_docsum|Nucleic Acids Res 33(17)], 2005 * Our approaches to annotation, gene calling etc are outlined in a series of [[SOPs|Standard Operating Procedures]]. 1b67f42f70859853c2cea292551847103c58ba30 1427 1426 2006-08-11T18:11:54Z FolkerMeyer 2 wikitext text/x-wiki With the growing number of genomes becoming available, a software environment is needed to produce accurate and consistent annotations. The SEED is that environment. We provide a public [http://explorer.theseed.org/FIG/index.cgi SEED-Viewer] that allows read-only access to the latest data and annotations. For users interested in editing and learning how to use the system, we also provide a [http://theseed.uchicago.edu/FIG/index.cgi Trial-SEED]. As described in our [[Annotating_1000_genomes|manifesto]] the [[Glossary#annotation|annotation]] is not performed on a gene by gene basis per genome, but rather by [[Glossary#subsystem|subsystem]] by an expert curator across many genomes at a time. We make all our software and data available for download and use on our [[DownloadPage]] page. * When using the SEED, please cite: Overbeek et al., [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16214803&query_hl=2&itool=pubmed_docsum|Nucleic Acids Res 33(17)], 2005 * Our approaches to annotation, gene calling etc are outlined in a series of [[SOPs|Standard Operating Procedures]]. ab7a633c5001325205085be11b2d4856d5fb7a14 0 1377 1433 2006-08-11T19:02:29Z FolkerMeyer 2 wikitext text/x-wiki <table> <tr> <th> Header Cell: Column 1 </th> <th> Header Cell: Column 2 </th> </tr> <tr> <td> Data Cell: Row2 Column1 </td> <td> Data Cell: Row2 Column2 </td> </tr> <tr> <td> Data Cell: Row3 Column1 </td> <td> Data Cell: Row3 Column1 </td> </tr> </table> <table> <tr> <td class="title" style="color: black;">The SEED: </td> <td class="title" style="color: black;"><div id="xxx" onclick="showtip();" class="showme" style="cursor: pointer;">... </div></td> <td class="title" style="color: black;"><div id="ooo" onclick="hidetip();" class="hideme" style="cursor: pointer;padding-right: 4px;">mighty oaks</div></td> <td class="title" style="color: black;"><a> from little acorns grow</td><td class="title" style="color: black; vertical-align: bottom; padding-left: 5px;"> <a style="font-size: 8pt; font-style: italic;">(English proverb)</a></td> </tr> </table> 148b2213f624f418444dc050259c59b86841b440 0 1371 1434 1388 2006-08-11T20:16:43Z FolkerMeyer 2 wikitext text/x-wiki == SEED standard operating procedures == To generate data that is usefull to the various communities involved in the process of annotation and use of annotations, we make available out standard operating procedures. * [[GeneCalling|Gene calling]] * Annotation ** Annotation of close strain sets ** Annotation of diverse genomes. 4e72ee7f5a6a64fcd0b30b48962cdcc63e9e5024 1439 1434 2006-08-13T16:04:38Z FolkerMeyer 2 wikitext text/x-wiki == SEED standard operating procedures == To generate data that is usefull to the various communities involved in the process of annotation and use of annotations, we make available out standard operating procedures. * [[GeneCalling|Gene calling]] * [[Annotation|Annotation]] ** Annotation of close strain sets ** Annotation of diverse genomes. 477c7096cfbbbe908978f8b33c55b78637e44263 1461 1439 2006-08-13T16:52:32Z 67.173.121.42 0 /* SEED standard operating procedures */ wikitext text/x-wiki == SEED standard operating procedures == To generate data that is usefull to the various communities involved in the process of annotation and use of annotations, we make available out standard operating procedures. * [[GeneCalling|Gene calling]] * [[Annotation|Annotation]] ** Annotation of close strain sets ** Annotation of diverse genomes. 3e41a17921ed2e8d659557b744eb786556a689aa 1462 1461 2006-08-13T17:25:18Z 67.173.121.42 0 /* SEED standard operating procedures */ wikitext text/x-wiki == SEED standard operating procedures == To generate data that is usefull to the various communities involved in the process of annotation and use of annotations, we make available out standard operating procedures. * [[GeneCalling|Gene calling]] * [[Annotation|Annotation]] ** Annotation of close strain sets ** Annotation of diverse genomes. 477c7096cfbbbe908978f8b33c55b78637e44263 0 1378 1435 2006-08-11T20:36:46Z FolkerMeyer 2 wikitext text/x-wiki Calling Genes: == Standard Operating Procedure == === Introduction === This procedure is designed to be used by members of the NMPDR and the SEED developers to call genes in two broad classes of genomes: • Genomes for NMPDR pathogens, which come from five sets of closely related strains of pathogens, and • Diverse genomes used to support comparative analysis. When we integrate diverse complete genomes, we often just take the genomes from RefSeq. Only in cases where the RefSeq gene calls require improvement do we apply similar procedures as for the NMPDR pathogens. This document describes the procedure used to call genes for NMPDR pathogens. === Summary of the procedure === The overall set of steps used to call genes is as follows: 1. Identify tRNAs: When we search for tRNAs in the diverse, non-NMPDR genomes, we use tRNAscan-SE, a tool developed by Sean Eddy, which we believe performs extremely well. However, for NMPDR pathogens, we maintain a library of all located tRNAs; locating the corresponding instances in new genomes is extremely straightforward. 2. Identify rRNAs: Again, for this we use a custom tool constructed by the NMPDR. Since the basic classes of rRNAs for each of the organisms curated by the NMPDR have been identified in several existing genomes, locating these rRNAs in new genomes is again completely straightforward. 3. Identify a set of expected genes: There is a set of “universal” genes and a number of families of highly conserved genes that are expected to be present in each of the NMPDR pathogens. We look for the genes candidates that are the most similar to these “universal” genes or matching the highly conserved gene families in each new genome, recording those instances that are found. 4. Use GLIMMER trained on the detected genes: We use the highly conserved gene candidates found in step (3.) as training set for GLIMMER 2, a tool developed and made available by TIGR. In most cases, we believe that the set of gene candidates identified by GLIMMER given a highly reliable training set (which we feel exist in the cases of NMPDR pathogens) should be a “superset” of the set of real genes (modulo a small rate of “false negatives”). 5. Resolve overlaps: We have developed a custom tool that resolves gene overlaps. Because we can use the gene-calls for a set of phylogenetically close organisms to validate the candidates gene calls in the new genome, we can reliably identify the vast majority of genes in steps 1--3 with high accuracy. Hence, we are confident that this overlap resolution tool performs well. 6. Backfill gaps: We check for potential short genes within any gaps exceeding 90 bp that remain after step 5. We do this by blasting the gaps between gene candidates against a collection of genomes from the immediate phylogenetic neighborhood (i.e., a fixed set of genomes for each of the general classes of NMPDR pathogens). Gene candidates that are detected are added to the calls from steps 1--5. In some cases, this step may add gene candidates that are not real; we therefore periodically review the calls in each set of close genomes for possible “false positives,” but in general, we would prefer to add a few too many genes, rather than leave out real ones. 7. Check Starts: A penultimate pass is made to adjust start positions using an algorithm based on seeking a consistent position in each of the sets of genomes curated by the NMPDR. The algorithm takes into account the start codon, the presence or absence of a ribosome binding site, and the ability to align candidate start positions with those in the existing set of close genomes. 8. Identification of potential frameshifts and pseudo-genes: As a last step, we run an automated tool that attempts to identify potential frameshifts and pseudo-genes. When these are detected, these features are recorded, along with the evidence supporting the assertion. Each of these steps generates a log entry summarizing the outcome. The final output constitutes a genome in a form that can be added to the SEED, and then into the NMPDR. === Details === ==== Step 1: Identify tRNAs ==== To locate the tRNAs and produce tbl/fasta entries, invoke find_instances –n User LibraryOfInstances SkeletalOrganismDirectory This tool assumes that the library contains instances of tRNAs from closely related genomes. It locates instances matching the tRNAs stored in the indicated library, updates the tbl and fasta file, adds corresponding assigned_functions entries, and logs the results. ==== Step 2: Identify rRNAs ==== To locate the tRNAs and produce tbl/fasta entries, invoke find_instances –n User LibraryOfInstances SkeletalOrganismDirectory This tool assumes that the library contains instances of rRNAs from closely related genomes. It locates instances matching the rRNAs stored in the indicated library, updates the tbl and fasta file, adds the corresponding assigned_functions entries, and logs the results. ==== Step 3: Identify a set of expected genes ==== The searching for and identifying protein-encoding genes is done in two steps: find_neighbors GenomeDirectory 20 found new > close.neighbors find_genes_based_on_neighbors GenomeDirectory found new < close.neighbors The first step takes DATA/FigFamsData and a genome directory (of the form xxxx.y) and locates the set of 20 closest genomes, calling a few genes in the process. The second command locates instances of of FIGfams that occur within the closely related genomes and in the new genome. In the case of closely-related NMPDR pathogens, we expect to locate 80-90% of the protein-encoding genes and to inherit annotations from existing genomes. ==== Step 4: Use GLIMMER trained on existing genes ==== The command recall_based_on_found GenomeDirectory close.neighbors > candidate_peg.tbl recalls the genes using GLIMMER, making sure that there is a gene for every protein-encoding gene (peg) that has already been called (with the same start). That is, this tool forms a superset of the previously called genes by merging the calls from a GLIMMER run trained using the existing set of protein-encoding gene-calls with the existing set. ==== Step 5: Resolve overlaps ==== By running resolve_overlaps GenomeDirectory candidate_peg.tbl we remove unacceptable overlaps between called genes and those determined by GLIMMER, and add them to the genes in GenomeDirectory. ==== Step 6: Backfill gaps ==== We then run backfill_gaps GenomeDirectory to search for possible genes in any gaps that appear to be unusually long. Here, we retain only genes that have similarity to genes that exist in other genomes (that are sufficiently distant from the new genome). ==== Step 7: Check Starts ==== We use adjust_starts GenomeDirectory to attempt to make starts consistent with those of genes in existing genomes. ==== Step 8: Identification of potential frameshifts and pseudo-genes ==== Finally, we run correct_frameshifts GenomeDirectory if we feel that we should attempt to automatically correct potential frameshifts. This will produce log entries documenting the “corrections”. If we prefer to simply add annotations to what appear to be fragments of genes (i.e., real pseudo-genes due to real frameshifts or partial genes due to assembly errors), we run instead annotate_potential_frameshifts GenomeDirectory which adds annotations describing the evidence for a potential frameshift. The decision to use one approach over the other is handled case by case. aef2f058c6f254255458d1fa0b2c6e5371e6ca8c 1436 1435 2006-08-11T20:37:10Z FolkerMeyer 2 wikitext text/x-wiki Calling Genes: == Standard Operating Procedure == === Introduction === This procedure is designed to be used by members of the NMPDR and the SEED developers to call genes in two broad classes of genomes: • Genomes for NMPDR pathogens, which come from five sets of closely related strains of pathogens, and • Diverse genomes used to support comparative analysis. When we integrate diverse complete genomes, we often just take the genomes from RefSeq. Only in cases where the RefSeq gene calls require improvement do we apply similar procedures as for the NMPDR pathogens. This document describes the procedure used to call genes for NMPDR pathogens. === Summary of the procedure === The overall set of steps used to call genes is as follows: 1. Identify tRNAs: When we search for tRNAs in the diverse, non-NMPDR genomes, we use tRNAscan-SE, a tool developed by Sean Eddy, which we believe performs extremely well. However, for NMPDR pathogens, we maintain a library of all located tRNAs; locating the corresponding instances in new genomes is extremely straightforward. 2. Identify rRNAs: Again, for this we use a custom tool constructed by the NMPDR. Since the basic classes of rRNAs for each of the organisms curated by the NMPDR have been identified in several existing genomes, locating these rRNAs in new genomes is again completely straightforward. 3. Identify a set of expected genes: There is a set of “universal” genes and a number of families of highly conserved genes that are expected to be present in each of the NMPDR pathogens. We look for the genes candidates that are the most similar to these “universal” genes or matching the highly conserved gene families in each new genome, recording those instances that are found. 4. Use GLIMMER trained on the detected genes: We use the highly conserved gene candidates found in step (3.) as training set for GLIMMER 2, a tool developed and made available by TIGR. In most cases, we believe that the set of gene candidates identified by GLIMMER given a highly reliable training set (which we feel exist in the cases of NMPDR pathogens) should be a “superset” of the set of real genes (modulo a small rate of “false negatives”). 5. Resolve overlaps: We have developed a custom tool that resolves gene overlaps. Because we can use the gene-calls for a set of phylogenetically close organisms to validate the candidates gene calls in the new genome, we can reliably identify the vast majority of genes in steps 1--3 with high accuracy. Hence, we are confident that this overlap resolution tool performs well. 6. Backfill gaps: We check for potential short genes within any gaps exceeding 90 bp that remain after step 5. We do this by blasting the gaps between gene candidates against a collection of genomes from the immediate phylogenetic neighborhood (i.e., a fixed set of genomes for each of the general classes of NMPDR pathogens). Gene candidates that are detected are added to the calls from steps 1--5. In some cases, this step may add gene candidates that are not real; we therefore periodically review the calls in each set of close genomes for possible “false positives,” but in general, we would prefer to add a few too many genes, rather than leave out real ones. 7. Check Starts: A penultimate pass is made to adjust start positions using an algorithm based on seeking a consistent position in each of the sets of genomes curated by the NMPDR. The algorithm takes into account the start codon, the presence or absence of a ribosome binding site, and the ability to align candidate start positions with those in the existing set of close genomes. 8. Identification of potential frameshifts and pseudo-genes: As a last step, we run an automated tool that attempts to identify potential frameshifts and pseudo-genes. When these are detected, these features are recorded, along with the evidence supporting the assertion. Each of these steps generates a log entry summarizing the outcome. The final output constitutes a genome in a form that can be added to the SEED, and then into the NMPDR. === Details === ==== Step 1: Identify tRNAs ==== To locate the tRNAs and produce tbl/fasta entries, invoke find_instances –n User LibraryOfInstances SkeletalOrganismDirectory This tool assumes that the library contains instances of tRNAs from closely related genomes. It locates instances matching the tRNAs stored in the indicated library, updates the tbl and fasta file, adds corresponding assigned_functions entries, and logs the results. ==== Step 2: Identify rRNAs ==== To locate the tRNAs and produce tbl/fasta entries, invoke find_instances –n User LibraryOfInstances SkeletalOrganismDirectory This tool assumes that the library contains instances of rRNAs from closely related genomes. It locates instances matching the rRNAs stored in the indicated library, updates the tbl and fasta file, adds the corresponding assigned_functions entries, and logs the results. ==== Step 3: Identify a set of expected genes ==== The searching for and identifying protein-encoding genes is done in two steps: find_neighbors GenomeDirectory 20 found new > close.neighbors find_genes_based_on_neighbors GenomeDirectory found new < close.neighbors The first step takes DATA/FigFamsData and a genome directory (of the form xxxx.y) and locates the set of 20 closest genomes, calling a few genes in the process. The second command locates instances of of FIGfams that occur within the closely related genomes and in the new genome. In the case of closely-related NMPDR pathogens, we expect to locate 80-90% of the protein-encoding genes and to inherit annotations from existing genomes. ==== Step 4: Use GLIMMER trained on existing genes ==== The command recall_based_on_found GenomeDirectory close.neighbors > candidate_peg.tbl recalls the genes using GLIMMER, making sure that there is a gene for every protein-encoding gene (peg) that has already been called (with the same start). That is, this tool forms a superset of the previously called genes by merging the calls from a GLIMMER run trained using the existing set of protein-encoding gene-calls with the existing set. ==== Step 5: Resolve overlaps ==== By running resolve_overlaps GenomeDirectory candidate_peg.tbl we remove unacceptable overlaps between called genes and those determined by GLIMMER, and add them to the genes in GenomeDirectory. ==== Step 6: Backfill gaps ==== We then run backfill_gaps GenomeDirectory to search for possible genes in any gaps that appear to be unusually long. Here, we retain only genes that have similarity to genes that exist in other genomes (that are sufficiently distant from the new genome). ==== Step 7: Check Starts ==== We use adjust_starts GenomeDirectory to attempt to make starts consistent with those of genes in existing genomes. ==== Step 8: Identification of potential frameshifts and pseudo-genes ==== Finally, we run correct_frameshifts GenomeDirectory if we feel that we should attempt to automatically correct potential frameshifts. This will produce log entries documenting the “corrections”. If we prefer to simply add annotations to what appear to be fragments of genes (i.e., real pseudo-genes due to real frameshifts or partial genes due to assembly errors), we run instead annotate_potential_frameshifts GenomeDirectory which adds annotations describing the evidence for a potential frameshift. The decision to use one approach over the other is handled case by case. 7223e29341790aa9e852c53e6c56f443ab67e543 0 1379 1440 2006-08-13T16:09:19Z FolkerMeyer 2 wikitext text/x-wiki == Annotation of Genomes: == === Standard Operating Procedure === === Introduction === This procedure describes the annotation process used by the SEED and NMPDR annotators and curators. Let us begin by discussing a number of terms that we use in this document: '''Functional Role''': The concept of functional role is both basic and primitive in the sense that we will not pretend to offer a precise definition. It corresponds roughly to a single logical role that a gene or gene product may play in the operation of a cell. Gene function: The function of a protein-encoding gene (PEG) is the functional role played by the product of the gene or an expression describing a set of roles played by the encoded protein. The operators used to construct expressions and the meanings associated with the operators are described in http://www.nmpdr.org/FIG/Html/SEED_functions.html Genes other than PEGs can also be assigned functions (e.g., SSU rRNA). However, in most cases the functions assigned to genes other than PEGs tend not to be problematic. This document will focus solely on annotation of PEGs. Assigning a gene function and annotation: Annotators assign gene functions to genes, and we call this process annotation. In most contexts, people use the term annotation to refer to assignments of function to the genes within a single organism. We certainly use the term in this sense, but we also use it to describe the process of assigning functions to corresponding genes from numerous genomes. Our basic approach to annotation is to ask our annotators to annotate the genes included in a subsystem (e.g., glycolysis) across all genomes. This process of annotation of the genes within a subsystem across a set of genomes, rather than annotation of genes within a single genome, allows our annotators to focus on a constrained set of functional roles and attempt to accurately identify exactly what variant, if any, of a subsystem exists in each of the genomes. We use the term annotation to refer to assigning functions to genes (either within a single organism or to a constrained set of gene/protein families across a set of organisms). This activity certainly is closely related to the construction of subsystems and protein families (which we call FIGfams), but we will describe those activities elsewhere. '''Subsystem''': A subsystem is a set of functional roles that an annotator has decided should be thought of as related. Frequently, subsystems represent the collection of functional roles that make up a metabolic pathway, a complex (e.g., the ribosome), or a class of proteins (e.g., two-component signal-transduction proteins within Staphylococcus aureus). A populated subsystem is a subsystem with an attached spreadsheet. The rows of the spreadsheet represent genomes and the columns represent the functional roles of the spreadsheet. Each cell contains the identifiers of genes from the corresponding genome the implement the specific functional role. That is, a populated subsystem specifies which genes implement instances of the subsystem in each of the genomes. The rows of a populated genome are assigned variant codes which describe which of a set of possible variants of the subsystem exist within each genome (special codes expressing a total absence of the subsystem or remaining uncertainty exist). Construction of a large set of curated populated subsystems is at the center of the NMPDR and SEED annotation efforts. '''FIGfam''': FIGfams are protein families generated by the Fellowship for Interpretation of Genomes (FIG). These families are based on the collection of subsystems, as well as correspondences between genes in closely related strains (we describe the construction of FIGfams in a separate SOP). The important properties of these families are as follows: 1. Two PEGs which both occur within a single FIGfam are believed to have the same function. 2. There is a decision procedure associated with the family which can be invoked to determine whether or not a gene can be “safely” assigned the function associated with the family. '''Metabolic Reconstruction''': When we use the term metabolic reconstruction of a given genome we will simply mean the set of populated subsystems that contain the genome, the PEGs (and their assigned functions) that are connected to functional roles in these populated subsystems, and the specific variant code associated with the genome in each of the populated subsystems. NMPDR pathogen genome: The NMPDR is responsible for five classes of genomes: 1. Campylobacter jejuni 2. Listeria monocytogenes 3. Staphylococcus aureus 4. Streptococcus pneumoniae and Streptococcus pyogenes 5. Pathogenic Vibrio We refer to these genomes as the NMPDR pathogens. The NMPDR carefully annotates some close relatives of these classes to provide accurate comparative context. Similarly, it includes a diverse collection of complete genomes that it annotates less accurately to provide context for comparative analysis. Now we can discuss what we mean by the annotations and the standard procedure for making those annotations. === The Annotation Procedure === The annotation of genomes begins after the genes have been identified and the genome has been integrated into a SEED environment. The annotation process then proceeds through the following steps: • Step 1: Use of FIGfams • Step 2: Use of Subsystems • Step 3: Annotation of Prophages • Step 4: Resolution of Conflicts • Step 5: Improvement of Annotation Via New Subsystems • Step 6: Continuous Refinement Via Analysis of Literature The following sections cover each of these steps in detail. We present the sequence of steps as commands issued from the command line. In fact, we are constructing a pipeline managed from a web interface that is intended to allow a relatively unskilled user to control the process. === Step 1: Use of FIGfams === For each new genome, we form a set of anticipated families by gathering all FIGfams with members in genomes from the same class. We begin the annotation by taking the anticipated families and searching for occurrences of these FIGfams within the new genome. This is achieved by invoking install_anticipated_functions User GenomeToBeAnnotated FileOfGenomesGivingContext Where User is the individual issuing the command, GenomeToBeAnnotated is the ID of the genome to be annotated (it is assumed that this genome has already been installed in the current SEED), and FileOfGenomesGivingContext is a file containing genome IDs (one per line) of the existing genomes from the same class. The effect of running this command will be to locate the instances of families when possible, to assign the appropriate function to the located genes, and to record detailed annotations of which FIGfam families were used as the basis for each annotation (along with the User and timestamps). ==== Step 2: Use of Subsystems ==== Once initial assignments based on FIGfams has been accomplished, it is possible to rapidly assess the presence and absence of subsystems (it is worth noting that every functional role within existing subsystems is covered by a FIGfam). The process begins with potentially_missed_assignments GenomeToBeAnnotated FileOfGenomesGivingContext This command will produce a list of assignments that may have been missed. This list is formed by looking at subsystems contained in each of the genomes that make up the context, checking for subsystems in which a majority (but not all) of the genes have corresponding genes in the new genome, and candidates for the missing genes can be located. The tool produces a list of possibly missed assignments that must be checked by an annotator. Once the list of possibly missed assignments has been processed, the following command can be run: add_to_subsystems User GenomeToBeAnnotated FileOfGenomesGivingContext This command will compute the set of subsystems from the context genomes for which all of the corresponding genes can be located in the new genome. This set of subsystems will then be split into two lists: 1. Some of the subsystems are marked as automatically extendable by their curators. For these subsystems, the new genome will be added to the populated subsystem. 2. For those subsystems that are not marked as automatically extendable, the fact that the new genome should be added to the subsystem will be recorded. Curators for these subsystems will be notified and asked to add the new genome. The tentative metabolic reconstruction is formed (including subsystems from both lists). ==== Step 3: Annotation of Prophages and Mobil Elements ==== For each class of NMPDR pathogen we maintain as features a list of prophages and other mobil elements. Execution of mark_features prophage User GenomeToBeAnnotated FileOfGenomesGivingContext mark_features mobil_element User GenomeToBeAnnotated FileOfGenomesGivingContext will cause instances of these prohages and other mobile elements to be detected and marked as features in the new genome. These annotations will be logged. ==== Step 4: Resolution of Conflicts ==== FIGfams are not always annotated consistently. This can happen in cases in which it is possible to assert that a set of genes have a common function, but for which disagreement remains about exactly how to label the role played by members of the family. In such cases, a functional role is associated with the FIGfam, but individual members of the family may have distinct (inconsistent) functions. The number of such instances is gradually dropping, but we have adopted the position that it is better to retain the inconsistency (reflecting real uncertainty) rather than enforcing a common function. Execution of the following command will produce a list of conflicts that should be examined by an annotator: potential_conflicts GenomeToBeAnnotated FileOfGenomesGivingContext ==== Step 5: Improvement of Annotation Via New Subsystems ==== Normal subsystem maintenance occurs constantly. The basic activity of our annotators is to extend existing subsystems and to define and populate new subsystems. These activities produce a gradual improvement in the quality of annotations for all genomes. All new annotations are logged as they are made. ==== Step 6: Continuous Refinement Via Analysis of Literature ==== Annotators should continuously review new literature, seeking cases in which gene functions can be improved based on new results. Sometimes, this results in improvements in function for a specific gene (and these results are then propagated to other members of the NMPDR pathogen class). More often, these new results are used as the basis for new subsystems and have a broader impact. e1c1f75f04371967b8bf67b212e29c59a1345176 1441 1440 2006-08-13T16:11:16Z FolkerMeyer 2 wikitext text/x-wiki == Annotation of Genomes: == === Standard Operating Procedure === === Introduction === This procedure describes the annotation process used by the SEED and NMPDR annotators and curators. Let us begin by discussing a number of terms that we use in this document: '''Functional Role''': The concept of functional role is both basic and primitive in the sense that we will not pretend to offer a precise definition. It corresponds roughly to a single logical role that a gene or gene product may play in the operation of a cell. Gene function: The function of a protein-encoding gene (PEG) is the functional role played by the product of the gene or an expression describing a set of roles played by the encoded protein. The operators used to construct expressions and the meanings associated with the operators are described in http://www.nmpdr.org/FIG/Html/SEED_functions.html Genes other than PEGs can also be assigned functions (e.g., SSU rRNA). However, in most cases the functions assigned to genes other than PEGs tend not to be problematic. This document will focus solely on annotation of PEGs. Assigning a gene function and annotation: Annotators assign gene functions to genes, and we call this process annotation. In most contexts, people use the term annotation to refer to assignments of function to the genes within a single organism. We certainly use the term in this sense, but we also use it to describe the process of assigning functions to corresponding genes from numerous genomes. Our basic approach to annotation is to ask our annotators to annotate the genes included in a subsystem (e.g., glycolysis) across all genomes. This process of annotation of the genes within a subsystem across a set of genomes, rather than annotation of genes within a single genome, allows our annotators to focus on a constrained set of functional roles and attempt to accurately identify exactly what variant, if any, of a subsystem exists in each of the genomes. We use the term annotation to refer to assigning functions to genes (either within a single organism or to a constrained set of gene/protein families across a set of organisms). This activity certainly is closely related to the construction of subsystems and protein families (which we call FIGfams), but we will describe those activities elsewhere. '''Subsystem''': A subsystem is a set of functional roles that an annotator has decided should be thought of as related. Frequently, subsystems represent the collection of functional roles that make up a metabolic pathway, a complex (e.g., the ribosome), or a class of proteins (e.g., two-component signal-transduction proteins within Staphylococcus aureus). A populated subsystem is a subsystem with an attached spreadsheet. The rows of the spreadsheet represent genomes and the columns represent the functional roles of the spreadsheet. Each cell contains the identifiers of genes from the corresponding genome the implement the specific functional role. That is, a populated subsystem specifies which genes implement instances of the subsystem in each of the genomes. The rows of a populated genome are assigned variant codes which describe which of a set of possible variants of the subsystem exist within each genome (special codes expressing a total absence of the subsystem or remaining uncertainty exist). Construction of a large set of curated populated subsystems is at the center of the NMPDR and SEED annotation efforts. '''FIGfam''': FIGfams are protein families generated by the Fellowship for Interpretation of Genomes (FIG). These families are based on the collection of subsystems, as well as correspondences between genes in closely related strains (we describe the construction of FIGfams in a separate SOP). The important properties of these families are as follows: 1. Two PEGs which both occur within a single FIGfam are believed to have the same function. 2. There is a decision procedure associated with the family which can be invoked to determine whether or not a gene can be “safely” assigned the function associated with the family. '''Metabolic Reconstruction''': When we use the term metabolic reconstruction of a given genome we will simply mean the set of populated subsystems that contain the genome, the PEGs (and their assigned functions) that are connected to functional roles in these populated subsystems, and the specific variant code associated with the genome in each of the populated subsystems. NMPDR pathogen genome: The NMPDR is responsible for five classes of genomes: # Campylobacter jejuni # Listeria monocytogenes # Staphylococcus aureus # Streptococcus pneumoniae and Streptococcus pyogenes # Pathogenic Vibrio We refer to these genomes as the NMPDR pathogens. The NMPDR carefully annotates some close relatives of these classes to provide accurate comparative context. Similarly, it includes a diverse collection of complete genomes that it annotates less accurately to provide context for comparative analysis. Now we can discuss what we mean by the annotations and the standard procedure for making those annotations. === The Annotation Procedure === The annotation of genomes begins after the genes have been identified and the genome has been integrated into a SEED environment. The annotation process then proceeds through the following steps: • Step 1: Use of FIGfams • Step 2: Use of Subsystems • Step 3: Annotation of Prophages • Step 4: Resolution of Conflicts • Step 5: Improvement of Annotation Via New Subsystems • Step 6: Continuous Refinement Via Analysis of Literature The following sections cover each of these steps in detail. We present the sequence of steps as commands issued from the command line. In fact, we are constructing a pipeline managed from a web interface that is intended to allow a relatively unskilled user to control the process. === Step 1: Use of FIGfams === For each new genome, we form a set of anticipated families by gathering all FIGfams with members in genomes from the same class. We begin the annotation by taking the anticipated families and searching for occurrences of these FIGfams within the new genome. This is achieved by invoking install_anticipated_functions User GenomeToBeAnnotated FileOfGenomesGivingContext Where User is the individual issuing the command, GenomeToBeAnnotated is the ID of the genome to be annotated (it is assumed that this genome has already been installed in the current SEED), and FileOfGenomesGivingContext is a file containing genome IDs (one per line) of the existing genomes from the same class. The effect of running this command will be to locate the instances of families when possible, to assign the appropriate function to the located genes, and to record detailed annotations of which FIGfam families were used as the basis for each annotation (along with the User and timestamps). ==== Step 2: Use of Subsystems ==== Once initial assignments based on FIGfams has been accomplished, it is possible to rapidly assess the presence and absence of subsystems (it is worth noting that every functional role within existing subsystems is covered by a FIGfam). The process begins with potentially_missed_assignments GenomeToBeAnnotated FileOfGenomesGivingContext This command will produce a list of assignments that may have been missed. This list is formed by looking at subsystems contained in each of the genomes that make up the context, checking for subsystems in which a majority (but not all) of the genes have corresponding genes in the new genome, and candidates for the missing genes can be located. The tool produces a list of possibly missed assignments that must be checked by an annotator. Once the list of possibly missed assignments has been processed, the following command can be run: add_to_subsystems User GenomeToBeAnnotated FileOfGenomesGivingContext This command will compute the set of subsystems from the context genomes for which all of the corresponding genes can be located in the new genome. This set of subsystems will then be split into two lists: 1. Some of the subsystems are marked as automatically extendable by their curators. For these subsystems, the new genome will be added to the populated subsystem. 2. For those subsystems that are not marked as automatically extendable, the fact that the new genome should be added to the subsystem will be recorded. Curators for these subsystems will be notified and asked to add the new genome. The tentative metabolic reconstruction is formed (including subsystems from both lists). ==== Step 3: Annotation of Prophages and Mobil Elements ==== For each class of NMPDR pathogen we maintain as features a list of prophages and other mobil elements. Execution of mark_features prophage User GenomeToBeAnnotated FileOfGenomesGivingContext mark_features mobil_element User GenomeToBeAnnotated FileOfGenomesGivingContext will cause instances of these prohages and other mobile elements to be detected and marked as features in the new genome. These annotations will be logged. ==== Step 4: Resolution of Conflicts ==== FIGfams are not always annotated consistently. This can happen in cases in which it is possible to assert that a set of genes have a common function, but for which disagreement remains about exactly how to label the role played by members of the family. In such cases, a functional role is associated with the FIGfam, but individual members of the family may have distinct (inconsistent) functions. The number of such instances is gradually dropping, but we have adopted the position that it is better to retain the inconsistency (reflecting real uncertainty) rather than enforcing a common function. Execution of the following command will produce a list of conflicts that should be examined by an annotator: potential_conflicts GenomeToBeAnnotated FileOfGenomesGivingContext ==== Step 5: Improvement of Annotation Via New Subsystems ==== Normal subsystem maintenance occurs constantly. The basic activity of our annotators is to extend existing subsystems and to define and populate new subsystems. These activities produce a gradual improvement in the quality of annotations for all genomes. All new annotations are logged as they are made. ==== Step 6: Continuous Refinement Via Analysis of Literature ==== Annotators should continuously review new literature, seeking cases in which gene functions can be improved based on new results. Sometimes, this results in improvements in function for a specific gene (and these results are then propagated to other members of the NMPDR pathogen class). More often, these new results are used as the basis for new subsystems and have a broader impact. 94711027ea3ab408c52dbe68ceb7828ac5f92b7a 1442 1441 2006-08-13T16:12:41Z FolkerMeyer 2 wikitext text/x-wiki == Annotation of Genomes: == === Standard Operating Procedure === === Introduction === This procedure describes the annotation process used by the SEED and NMPDR annotators and curators. Let us begin by discussing a number of terms that we use in this document: '''Functional Role''': The concept of functional role is both basic and primitive in the sense that we will not pretend to offer a precise definition. It corresponds roughly to a single logical role that a gene or gene product may play in the operation of a cell. Gene function: The function of a protein-encoding gene (PEG) is the functional role played by the product of the gene or an expression describing a set of roles played by the encoded protein. The operators used to construct expressions and the meanings associated with the operators are described in http://www.nmpdr.org/FIG/Html/SEED_functions.html Genes other than PEGs can also be assigned functions (e.g., SSU rRNA). However, in most cases the functions assigned to genes other than PEGs tend not to be problematic. This document will focus solely on annotation of PEGs. Assigning a gene function and annotation: Annotators assign gene functions to genes, and we call this process annotation. In most contexts, people use the term annotation to refer to assignments of function to the genes within a single organism. We certainly use the term in this sense, but we also use it to describe the process of assigning functions to corresponding genes from numerous genomes. Our basic approach to annotation is to ask our annotators to annotate the genes included in a subsystem (e.g., glycolysis) across all genomes. This process of annotation of the genes within a subsystem across a set of genomes, rather than annotation of genes within a single genome, allows our annotators to focus on a constrained set of functional roles and attempt to accurately identify exactly what variant, if any, of a subsystem exists in each of the genomes. We use the term annotation to refer to assigning functions to genes (either within a single organism or to a constrained set of gene/protein families across a set of organisms). This activity certainly is closely related to the construction of subsystems and protein families (which we call FIGfams), but we will describe those activities elsewhere. '''Subsystem''': A subsystem is a set of functional roles that an annotator has decided should be thought of as related. Frequently, subsystems represent the collection of functional roles that make up a metabolic pathway, a complex (e.g., the ribosome), or a class of proteins (e.g., two-component signal-transduction proteins within Staphylococcus aureus). A populated subsystem is a subsystem with an attached spreadsheet. The rows of the spreadsheet represent genomes and the columns represent the functional roles of the spreadsheet. Each cell contains the identifiers of genes from the corresponding genome the implement the specific functional role. That is, a populated subsystem specifies which genes implement instances of the subsystem in each of the genomes. The rows of a populated genome are assigned variant codes which describe which of a set of possible variants of the subsystem exist within each genome (special codes expressing a total absence of the subsystem or remaining uncertainty exist). Construction of a large set of curated populated subsystems is at the center of the NMPDR and SEED annotation efforts. '''FIGfam''': FIGfams are protein families generated by the Fellowship for Interpretation of Genomes (FIG). These families are based on the collection of subsystems, as well as correspondences between genes in closely related strains (we describe the construction of FIGfams in a separate SOP). The important properties of these families are as follows: # Two PEGs which both occur within a single FIGfam are believed to have the same function. # There is a decision procedure associated with the family which can be invoked to determine whether or not a gene can be “safely” assigned the function associated with the family. '''Metabolic Reconstruction''': When we use the term metabolic reconstruction of a given genome we will simply mean the set of populated subsystems that contain the genome, the PEGs (and their assigned functions) that are connected to functional roles in these populated subsystems, and the specific variant code associated with the genome in each of the populated subsystems. NMPDR pathogen genome: The NMPDR is responsible for five classes of genomes: # Campylobacter jejuni # Listeria monocytogenes # Staphylococcus aureus # Streptococcus pneumoniae and Streptococcus pyogenes # Pathogenic Vibrio We refer to these genomes as the NMPDR pathogens. The NMPDR carefully annotates some close relatives of these classes to provide accurate comparative context. Similarly, it includes a diverse collection of complete genomes that it annotates less accurately to provide context for comparative analysis. Now we can discuss what we mean by the annotations and the standard procedure for making those annotations. === The Annotation Procedure === The annotation of genomes begins after the genes have been identified and the genome has been integrated into a SEED environment. The annotation process then proceeds through the following steps: Step #: Use of FIGfams Step #: Use of Subsystems • Step 3: Annotation of Prophages • Step 4: Resolution of Conflicts • Step 5: Improvement of Annotation Via New Subsystems • Step 6: Continuous Refinement Via Analysis of Literature The following sections cover each of these steps in detail. We present the sequence of steps as commands issued from the command line. In fact, we are constructing a pipeline managed from a web interface that is intended to allow a relatively unskilled user to control the process. ==== Step 1: Use of FIGfams ==== For each new genome, we form a set of anticipated families by gathering all FIGfams with members in genomes from the same class. We begin the annotation by taking the anticipated families and searching for occurrences of these FIGfams within the new genome. This is achieved by invoking install_anticipated_functions User GenomeToBeAnnotated FileOfGenomesGivingContext Where User is the individual issuing the command, GenomeToBeAnnotated is the ID of the genome to be annotated (it is assumed that this genome has already been installed in the current SEED), and FileOfGenomesGivingContext is a file containing genome IDs (one per line) of the existing genomes from the same class. The effect of running this command will be to locate the instances of families when possible, to assign the appropriate function to the located genes, and to record detailed annotations of which FIGfam families were used as the basis for each annotation (along with the User and timestamps). ==== Step 2: Use of Subsystems ==== Once initial assignments based on FIGfams has been accomplished, it is possible to rapidly assess the presence and absence of subsystems (it is worth noting that every functional role within existing subsystems is covered by a FIGfam). The process begins with potentially_missed_assignments GenomeToBeAnnotated FileOfGenomesGivingContext This command will produce a list of assignments that may have been missed. This list is formed by looking at subsystems contained in each of the genomes that make up the context, checking for subsystems in which a majority (but not all) of the genes have corresponding genes in the new genome, and candidates for the missing genes can be located. The tool produces a list of possibly missed assignments that must be checked by an annotator. Once the list of possibly missed assignments has been processed, the following command can be run: add_to_subsystems User GenomeToBeAnnotated FileOfGenomesGivingContext This command will compute the set of subsystems from the context genomes for which all of the corresponding genes can be located in the new genome. This set of subsystems will then be split into two lists: 1. Some of the subsystems are marked as automatically extendable by their curators. For these subsystems, the new genome will be added to the populated subsystem. 2. For those subsystems that are not marked as automatically extendable, the fact that the new genome should be added to the subsystem will be recorded. Curators for these subsystems will be notified and asked to add the new genome. The tentative metabolic reconstruction is formed (including subsystems from both lists). ==== Step 3: Annotation of Prophages and Mobil Elements ==== For each class of NMPDR pathogen we maintain as features a list of prophages and other mobil elements. Execution of mark_features prophage User GenomeToBeAnnotated FileOfGenomesGivingContext mark_features mobil_element User GenomeToBeAnnotated FileOfGenomesGivingContext will cause instances of these prohages and other mobile elements to be detected and marked as features in the new genome. These annotations will be logged. ==== Step 4: Resolution of Conflicts ==== FIGfams are not always annotated consistently. This can happen in cases in which it is possible to assert that a set of genes have a common function, but for which disagreement remains about exactly how to label the role played by members of the family. In such cases, a functional role is associated with the FIGfam, but individual members of the family may have distinct (inconsistent) functions. The number of such instances is gradually dropping, but we have adopted the position that it is better to retain the inconsistency (reflecting real uncertainty) rather than enforcing a common function. Execution of the following command will produce a list of conflicts that should be examined by an annotator: potential_conflicts GenomeToBeAnnotated FileOfGenomesGivingContext ==== Step 5: Improvement of Annotation Via New Subsystems ==== Normal subsystem maintenance occurs constantly. The basic activity of our annotators is to extend existing subsystems and to define and populate new subsystems. These activities produce a gradual improvement in the quality of annotations for all genomes. All new annotations are logged as they are made. ==== Step 6: Continuous Refinement Via Analysis of Literature ==== Annotators should continuously review new literature, seeking cases in which gene functions can be improved based on new results. Sometimes, this results in improvements in function for a specific gene (and these results are then propagated to other members of the NMPDR pathogen class). More often, these new results are used as the basis for new subsystems and have a broader impact. a67905485a74ae450554c8b4a07e6ce4c7112902 1443 1442 2006-08-13T16:13:20Z FolkerMeyer 2 wikitext text/x-wiki == Annotation of Genomes: == === Standard Operating Procedure === === Introduction === This procedure describes the annotation process used by the SEED and NMPDR annotators and curators. Let us begin by discussing a number of terms that we use in this document: '''Functional Role''': The concept of functional role is both basic and primitive in the sense that we will not pretend to offer a precise definition. It corresponds roughly to a single logical role that a gene or gene product may play in the operation of a cell. Gene function: The function of a protein-encoding gene (PEG) is the functional role played by the product of the gene or an expression describing a set of roles played by the encoded protein. The operators used to construct expressions and the meanings associated with the operators are described in http://www.nmpdr.org/FIG/Html/SEED_functions.html Genes other than PEGs can also be assigned functions (e.g., SSU rRNA). However, in most cases the functions assigned to genes other than PEGs tend not to be problematic. This document will focus solely on annotation of PEGs. Assigning a gene function and annotation: Annotators assign gene functions to genes, and we call this process annotation. In most contexts, people use the term annotation to refer to assignments of function to the genes within a single organism. We certainly use the term in this sense, but we also use it to describe the process of assigning functions to corresponding genes from numerous genomes. Our basic approach to annotation is to ask our annotators to annotate the genes included in a subsystem (e.g., glycolysis) across all genomes. This process of annotation of the genes within a subsystem across a set of genomes, rather than annotation of genes within a single genome, allows our annotators to focus on a constrained set of functional roles and attempt to accurately identify exactly what variant, if any, of a subsystem exists in each of the genomes. We use the term annotation to refer to assigning functions to genes (either within a single organism or to a constrained set of gene/protein families across a set of organisms). This activity certainly is closely related to the construction of subsystems and protein families (which we call FIGfams), but we will describe those activities elsewhere. '''Subsystem''': A subsystem is a set of functional roles that an annotator has decided should be thought of as related. Frequently, subsystems represent the collection of functional roles that make up a metabolic pathway, a complex (e.g., the ribosome), or a class of proteins (e.g., two-component signal-transduction proteins within Staphylococcus aureus). A populated subsystem is a subsystem with an attached spreadsheet. The rows of the spreadsheet represent genomes and the columns represent the functional roles of the spreadsheet. Each cell contains the identifiers of genes from the corresponding genome the implement the specific functional role. That is, a populated subsystem specifies which genes implement instances of the subsystem in each of the genomes. The rows of a populated genome are assigned variant codes which describe which of a set of possible variants of the subsystem exist within each genome (special codes expressing a total absence of the subsystem or remaining uncertainty exist). Construction of a large set of curated populated subsystems is at the center of the NMPDR and SEED annotation efforts. '''FIGfam''': FIGfams are protein families generated by the Fellowship for Interpretation of Genomes (FIG). These families are based on the collection of subsystems, as well as correspondences between genes in closely related strains (we describe the construction of FIGfams in a separate SOP). The important properties of these families are as follows: # Two PEGs which both occur within a single FIGfam are believed to have the same function. # There is a decision procedure associated with the family which can be invoked to determine whether or not a gene can be “safely” assigned the function associated with the family. '''Metabolic Reconstruction''': When we use the term metabolic reconstruction of a given genome we will simply mean the set of populated subsystems that contain the genome, the PEGs (and their assigned functions) that are connected to functional roles in these populated subsystems, and the specific variant code associated with the genome in each of the populated subsystems. NMPDR pathogen genome: The NMPDR is responsible for five classes of genomes: # Campylobacter jejuni # Listeria monocytogenes # Staphylococcus aureus # Streptococcus pneumoniae and Streptococcus pyogenes # Pathogenic Vibrio We refer to these genomes as the NMPDR pathogens. The NMPDR carefully annotates some close relatives of these classes to provide accurate comparative context. Similarly, it includes a diverse collection of complete genomes that it annotates less accurately to provide context for comparative analysis. Now we can discuss what we mean by the annotations and the standard procedure for making those annotations. === The Annotation Procedure === The annotation of genomes begins after the genes have been identified and the genome has been integrated into a SEED environment. The annotation process then proceeds through the following steps: #: Use of FIGfams #: Use of Subsystems #: Annotation of Prophages #: Resolution of Conflicts #: Improvement of Annotation Via New Subsystems #: Continuous Refinement Via Analysis of Literature The following sections cover each of these steps in detail. We present the sequence of steps as commands issued from the command line. In fact, we are constructing a pipeline managed from a web interface that is intended to allow a relatively unskilled user to control the process. ==== Step 1: Use of FIGfams ==== For each new genome, we form a set of anticipated families by gathering all FIGfams with members in genomes from the same class. We begin the annotation by taking the anticipated families and searching for occurrences of these FIGfams within the new genome. This is achieved by invoking install_anticipated_functions User GenomeToBeAnnotated FileOfGenomesGivingContext Where User is the individual issuing the command, GenomeToBeAnnotated is the ID of the genome to be annotated (it is assumed that this genome has already been installed in the current SEED), and FileOfGenomesGivingContext is a file containing genome IDs (one per line) of the existing genomes from the same class. The effect of running this command will be to locate the instances of families when possible, to assign the appropriate function to the located genes, and to record detailed annotations of which FIGfam families were used as the basis for each annotation (along with the User and timestamps). ==== Step 2: Use of Subsystems ==== Once initial assignments based on FIGfams has been accomplished, it is possible to rapidly assess the presence and absence of subsystems (it is worth noting that every functional role within existing subsystems is covered by a FIGfam). The process begins with potentially_missed_assignments GenomeToBeAnnotated FileOfGenomesGivingContext This command will produce a list of assignments that may have been missed. This list is formed by looking at subsystems contained in each of the genomes that make up the context, checking for subsystems in which a majority (but not all) of the genes have corresponding genes in the new genome, and candidates for the missing genes can be located. The tool produces a list of possibly missed assignments that must be checked by an annotator. Once the list of possibly missed assignments has been processed, the following command can be run: add_to_subsystems User GenomeToBeAnnotated FileOfGenomesGivingContext This command will compute the set of subsystems from the context genomes for which all of the corresponding genes can be located in the new genome. This set of subsystems will then be split into two lists: 1. Some of the subsystems are marked as automatically extendable by their curators. For these subsystems, the new genome will be added to the populated subsystem. 2. For those subsystems that are not marked as automatically extendable, the fact that the new genome should be added to the subsystem will be recorded. Curators for these subsystems will be notified and asked to add the new genome. The tentative metabolic reconstruction is formed (including subsystems from both lists). ==== Step 3: Annotation of Prophages and Mobil Elements ==== For each class of NMPDR pathogen we maintain as features a list of prophages and other mobil elements. Execution of mark_features prophage User GenomeToBeAnnotated FileOfGenomesGivingContext mark_features mobil_element User GenomeToBeAnnotated FileOfGenomesGivingContext will cause instances of these prohages and other mobile elements to be detected and marked as features in the new genome. These annotations will be logged. ==== Step 4: Resolution of Conflicts ==== FIGfams are not always annotated consistently. This can happen in cases in which it is possible to assert that a set of genes have a common function, but for which disagreement remains about exactly how to label the role played by members of the family. In such cases, a functional role is associated with the FIGfam, but individual members of the family may have distinct (inconsistent) functions. The number of such instances is gradually dropping, but we have adopted the position that it is better to retain the inconsistency (reflecting real uncertainty) rather than enforcing a common function. Execution of the following command will produce a list of conflicts that should be examined by an annotator: potential_conflicts GenomeToBeAnnotated FileOfGenomesGivingContext ==== Step 5: Improvement of Annotation Via New Subsystems ==== Normal subsystem maintenance occurs constantly. The basic activity of our annotators is to extend existing subsystems and to define and populate new subsystems. These activities produce a gradual improvement in the quality of annotations for all genomes. All new annotations are logged as they are made. ==== Step 6: Continuous Refinement Via Analysis of Literature ==== Annotators should continuously review new literature, seeking cases in which gene functions can be improved based on new results. Sometimes, this results in improvements in function for a specific gene (and these results are then propagated to other members of the NMPDR pathogen class). More often, these new results are used as the basis for new subsystems and have a broader impact. 83649fd4becdc62365c00910d3d0a723ebf5a3a3 1444 1443 2006-08-13T16:13:42Z FolkerMeyer 2 wikitext text/x-wiki == Annotation of Genomes: == === Standard Operating Procedure === === Introduction === This procedure describes the annotation process used by the SEED and NMPDR annotators and curators. Let us begin by discussing a number of terms that we use in this document: '''Functional Role''': The concept of functional role is both basic and primitive in the sense that we will not pretend to offer a precise definition. It corresponds roughly to a single logical role that a gene or gene product may play in the operation of a cell. Gene function: The function of a protein-encoding gene (PEG) is the functional role played by the product of the gene or an expression describing a set of roles played by the encoded protein. The operators used to construct expressions and the meanings associated with the operators are described in http://www.nmpdr.org/FIG/Html/SEED_functions.html Genes other than PEGs can also be assigned functions (e.g., SSU rRNA). However, in most cases the functions assigned to genes other than PEGs tend not to be problematic. This document will focus solely on annotation of PEGs. Assigning a gene function and annotation: Annotators assign gene functions to genes, and we call this process annotation. In most contexts, people use the term annotation to refer to assignments of function to the genes within a single organism. We certainly use the term in this sense, but we also use it to describe the process of assigning functions to corresponding genes from numerous genomes. Our basic approach to annotation is to ask our annotators to annotate the genes included in a subsystem (e.g., glycolysis) across all genomes. This process of annotation of the genes within a subsystem across a set of genomes, rather than annotation of genes within a single genome, allows our annotators to focus on a constrained set of functional roles and attempt to accurately identify exactly what variant, if any, of a subsystem exists in each of the genomes. We use the term annotation to refer to assigning functions to genes (either within a single organism or to a constrained set of gene/protein families across a set of organisms). This activity certainly is closely related to the construction of subsystems and protein families (which we call FIGfams), but we will describe those activities elsewhere. '''Subsystem''': A subsystem is a set of functional roles that an annotator has decided should be thought of as related. Frequently, subsystems represent the collection of functional roles that make up a metabolic pathway, a complex (e.g., the ribosome), or a class of proteins (e.g., two-component signal-transduction proteins within Staphylococcus aureus). A populated subsystem is a subsystem with an attached spreadsheet. The rows of the spreadsheet represent genomes and the columns represent the functional roles of the spreadsheet. Each cell contains the identifiers of genes from the corresponding genome the implement the specific functional role. That is, a populated subsystem specifies which genes implement instances of the subsystem in each of the genomes. The rows of a populated genome are assigned variant codes which describe which of a set of possible variants of the subsystem exist within each genome (special codes expressing a total absence of the subsystem or remaining uncertainty exist). Construction of a large set of curated populated subsystems is at the center of the NMPDR and SEED annotation efforts. '''FIGfam''': FIGfams are protein families generated by the Fellowship for Interpretation of Genomes (FIG). These families are based on the collection of subsystems, as well as correspondences between genes in closely related strains (we describe the construction of FIGfams in a separate SOP). The important properties of these families are as follows: # Two PEGs which both occur within a single FIGfam are believed to have the same function. # There is a decision procedure associated with the family which can be invoked to determine whether or not a gene can be “safely” assigned the function associated with the family. '''Metabolic Reconstruction''': When we use the term metabolic reconstruction of a given genome we will simply mean the set of populated subsystems that contain the genome, the PEGs (and their assigned functions) that are connected to functional roles in these populated subsystems, and the specific variant code associated with the genome in each of the populated subsystems. NMPDR pathogen genome: The NMPDR is responsible for five classes of genomes: # Campylobacter jejuni # Listeria monocytogenes # Staphylococcus aureus # Streptococcus pneumoniae and Streptococcus pyogenes # Pathogenic Vibrio We refer to these genomes as the NMPDR pathogens. The NMPDR carefully annotates some close relatives of these classes to provide accurate comparative context. Similarly, it includes a diverse collection of complete genomes that it annotates less accurately to provide context for comparative analysis. Now we can discuss what we mean by the annotations and the standard procedure for making those annotations. === The Annotation Procedure === The annotation of genomes begins after the genes have been identified and the genome has been integrated into a SEED environment. The annotation process then proceeds through the following steps: # Use of FIGfams # Use of Subsystems # Annotation of Prophages # Resolution of Conflicts # Improvement of Annotation Via New Subsystems # Continuous Refinement Via Analysis of Literature The following sections cover each of these steps in detail. We present the sequence of steps as commands issued from the command line. In fact, we are constructing a pipeline managed from a web interface that is intended to allow a relatively unskilled user to control the process. ==== Step 1: Use of FIGfams ==== For each new genome, we form a set of anticipated families by gathering all FIGfams with members in genomes from the same class. We begin the annotation by taking the anticipated families and searching for occurrences of these FIGfams within the new genome. This is achieved by invoking install_anticipated_functions User GenomeToBeAnnotated FileOfGenomesGivingContext Where User is the individual issuing the command, GenomeToBeAnnotated is the ID of the genome to be annotated (it is assumed that this genome has already been installed in the current SEED), and FileOfGenomesGivingContext is a file containing genome IDs (one per line) of the existing genomes from the same class. The effect of running this command will be to locate the instances of families when possible, to assign the appropriate function to the located genes, and to record detailed annotations of which FIGfam families were used as the basis for each annotation (along with the User and timestamps). ==== Step 2: Use of Subsystems ==== Once initial assignments based on FIGfams has been accomplished, it is possible to rapidly assess the presence and absence of subsystems (it is worth noting that every functional role within existing subsystems is covered by a FIGfam). The process begins with potentially_missed_assignments GenomeToBeAnnotated FileOfGenomesGivingContext This command will produce a list of assignments that may have been missed. This list is formed by looking at subsystems contained in each of the genomes that make up the context, checking for subsystems in which a majority (but not all) of the genes have corresponding genes in the new genome, and candidates for the missing genes can be located. The tool produces a list of possibly missed assignments that must be checked by an annotator. Once the list of possibly missed assignments has been processed, the following command can be run: add_to_subsystems User GenomeToBeAnnotated FileOfGenomesGivingContext This command will compute the set of subsystems from the context genomes for which all of the corresponding genes can be located in the new genome. This set of subsystems will then be split into two lists: 1. Some of the subsystems are marked as automatically extendable by their curators. For these subsystems, the new genome will be added to the populated subsystem. 2. For those subsystems that are not marked as automatically extendable, the fact that the new genome should be added to the subsystem will be recorded. Curators for these subsystems will be notified and asked to add the new genome. The tentative metabolic reconstruction is formed (including subsystems from both lists). ==== Step 3: Annotation of Prophages and Mobil Elements ==== For each class of NMPDR pathogen we maintain as features a list of prophages and other mobil elements. Execution of mark_features prophage User GenomeToBeAnnotated FileOfGenomesGivingContext mark_features mobil_element User GenomeToBeAnnotated FileOfGenomesGivingContext will cause instances of these prohages and other mobile elements to be detected and marked as features in the new genome. These annotations will be logged. ==== Step 4: Resolution of Conflicts ==== FIGfams are not always annotated consistently. This can happen in cases in which it is possible to assert that a set of genes have a common function, but for which disagreement remains about exactly how to label the role played by members of the family. In such cases, a functional role is associated with the FIGfam, but individual members of the family may have distinct (inconsistent) functions. The number of such instances is gradually dropping, but we have adopted the position that it is better to retain the inconsistency (reflecting real uncertainty) rather than enforcing a common function. Execution of the following command will produce a list of conflicts that should be examined by an annotator: potential_conflicts GenomeToBeAnnotated FileOfGenomesGivingContext ==== Step 5: Improvement of Annotation Via New Subsystems ==== Normal subsystem maintenance occurs constantly. The basic activity of our annotators is to extend existing subsystems and to define and populate new subsystems. These activities produce a gradual improvement in the quality of annotations for all genomes. All new annotations are logged as they are made. ==== Step 6: Continuous Refinement Via Analysis of Literature ==== Annotators should continuously review new literature, seeking cases in which gene functions can be improved based on new results. Sometimes, this results in improvements in function for a specific gene (and these results are then propagated to other members of the NMPDR pathogen class). More often, these new results are used as the basis for new subsystems and have a broader impact. bfa7c1820023b6a325d56e13fa787f7bb4bd8f00 1445 1444 2006-08-13T16:14:25Z FolkerMeyer 2 wikitext text/x-wiki == Annotation of Genomes: == === Standard Operating Procedure === === Introduction === This procedure describes the annotation process used by the SEED and NMPDR annotators and curators. Let us begin by discussing a number of terms that we use in this document: '''Functional Role''': The concept of functional role is both basic and primitive in the sense that we will not pretend to offer a precise definition. It corresponds roughly to a single logical role that a gene or gene product may play in the operation of a cell. Gene function: The function of a protein-encoding gene (PEG) is the functional role played by the product of the gene or an expression describing a set of roles played by the encoded protein. The operators used to construct expressions and the meanings associated with the operators are described in http://www.nmpdr.org/FIG/Html/SEED_functions.html Genes other than PEGs can also be assigned functions (e.g., SSU rRNA). However, in most cases the functions assigned to genes other than PEGs tend not to be problematic. This document will focus solely on annotation of PEGs. Assigning a gene function and annotation: Annotators assign gene functions to genes, and we call this process annotation. In most contexts, people use the term annotation to refer to assignments of function to the genes within a single organism. We certainly use the term in this sense, but we also use it to describe the process of assigning functions to corresponding genes from numerous genomes. Our basic approach to annotation is to ask our annotators to annotate the genes included in a subsystem (e.g., glycolysis) across all genomes. This process of annotation of the genes within a subsystem across a set of genomes, rather than annotation of genes within a single genome, allows our annotators to focus on a constrained set of functional roles and attempt to accurately identify exactly what variant, if any, of a subsystem exists in each of the genomes. We use the term annotation to refer to assigning functions to genes (either within a single organism or to a constrained set of gene/protein families across a set of organisms). This activity certainly is closely related to the construction of subsystems and protein families (which we call FIGfams), but we will describe those activities elsewhere. '''Subsystem''': A subsystem is a set of functional roles that an annotator has decided should be thought of as related. Frequently, subsystems represent the collection of functional roles that make up a metabolic pathway, a complex (e.g., the ribosome), or a class of proteins (e.g., two-component signal-transduction proteins within Staphylococcus aureus). A populated subsystem is a subsystem with an attached spreadsheet. The rows of the spreadsheet represent genomes and the columns represent the functional roles of the spreadsheet. Each cell contains the identifiers of genes from the corresponding genome the implement the specific functional role. That is, a populated subsystem specifies which genes implement instances of the subsystem in each of the genomes. The rows of a populated genome are assigned variant codes which describe which of a set of possible variants of the subsystem exist within each genome (special codes expressing a total absence of the subsystem or remaining uncertainty exist). Construction of a large set of curated populated subsystems is at the center of the NMPDR and SEED annotation efforts. '''FIGfam''': FIGfams are protein families generated by the Fellowship for Interpretation of Genomes (FIG). These families are based on the collection of subsystems, as well as correspondences between genes in closely related strains (we describe the construction of FIGfams in a separate SOP). The important properties of these families are as follows: # Two PEGs which both occur within a single FIGfam are believed to have the same function. # There is a decision procedure associated with the family which can be invoked to determine whether or not a gene can be “safely” assigned the function associated with the family. '''Metabolic Reconstruction''': When we use the term metabolic reconstruction of a given genome we will simply mean the set of populated subsystems that contain the genome, the PEGs (and their assigned functions) that are connected to functional roles in these populated subsystems, and the specific variant code associated with the genome in each of the populated subsystems. NMPDR pathogen genome: The NMPDR is responsible for five classes of genomes: # Campylobacter jejuni # Listeria monocytogenes # Staphylococcus aureus # Streptococcus pneumoniae and Streptococcus pyogenes # Pathogenic Vibrio We refer to these genomes as the NMPDR pathogens. The NMPDR carefully annotates some close relatives of these classes to provide accurate comparative context. Similarly, it includes a diverse collection of complete genomes that it annotates less accurately to provide context for comparative analysis. Now we can discuss what we mean by the annotations and the standard procedure for making those annotations. === The Annotation Procedure === The annotation of genomes begins after the genes have been identified and the genome has been integrated into a SEED environment. The annotation process then proceeds through the following steps: # Use of FIGfams # Use of Subsystems # Annotation of Prophages # Resolution of Conflicts # Improvement of Annotation Via New Subsystems # Continuous Refinement Via Analysis of Literature The following sections cover each of these steps in detail. We present the sequence of steps as commands issued from the command line. In fact, we are constructing a pipeline managed from a web interface that is intended to allow a relatively unskilled user to control the process. ==== Step 1: Use of FIGfams ==== For each new genome, we form a set of anticipated families by gathering all FIGfams with members in genomes from the same class. We begin the annotation by taking the anticipated families and searching for occurrences of these FIGfams within the new genome. This is achieved by invoking install_anticipated_functions User GenomeToBeAnnotated FileOfGenomesGivingContext Where User is the individual issuing the command, GenomeToBeAnnotated is the ID of the genome to be annotated (it is assumed that this genome has already been installed in the current SEED), and FileOfGenomesGivingContext is a file containing genome IDs (one per line) of the existing genomes from the same class. The effect of running this command will be to locate the instances of families when possible, to assign the appropriate function to the located genes, and to record detailed annotations of which FIGfam families were used as the basis for each annotation (along with the User and timestamps). ==== Step 2: Use of Subsystems ==== Once initial assignments based on FIGfams has been accomplished, it is possible to rapidly assess the presence and absence of subsystems (it is worth noting that every functional role within existing subsystems is covered by a FIGfam). The process begins with potentially_missed_assignments GenomeToBeAnnotated FileOfGenomesGivingContext This command will produce a list of assignments that may have been missed. This list is formed by looking at subsystems contained in each of the genomes that make up the context, checking for subsystems in which a majority (but not all) of the genes have corresponding genes in the new genome, and candidates for the missing genes can be located. The tool produces a list of possibly missed assignments that must be checked by an annotator. Once the list of possibly missed assignments has been processed, the following command can be run: add_to_subsystems User GenomeToBeAnnotated FileOfGenomesGivingContext This command will compute the set of subsystems from the context genomes for which all of the corresponding genes can be located in the new genome. This set of subsystems will then be split into two lists: # Some of the subsystems are marked as automatically extendable by their curators. For these subsystems, the new genome will be added to the populated subsystem. # For those subsystems that are not marked as automatically extendable, the fact that the new genome should be added to the subsystem will be recorded. Curators for these subsystems will be notified and asked to add the new genome. The tentative metabolic reconstruction is formed (including subsystems from both lists). ==== Step 3: Annotation of Prophages and Mobil Elements ==== For each class of NMPDR pathogen we maintain as features a list of prophages and other mobil elements. Execution of mark_features prophage User GenomeToBeAnnotated FileOfGenomesGivingContext mark_features mobil_element User GenomeToBeAnnotated FileOfGenomesGivingContext will cause instances of these prohages and other mobile elements to be detected and marked as features in the new genome. These annotations will be logged. ==== Step 4: Resolution of Conflicts ==== FIGfams are not always annotated consistently. This can happen in cases in which it is possible to assert that a set of genes have a common function, but for which disagreement remains about exactly how to label the role played by members of the family. In such cases, a functional role is associated with the FIGfam, but individual members of the family may have distinct (inconsistent) functions. The number of such instances is gradually dropping, but we have adopted the position that it is better to retain the inconsistency (reflecting real uncertainty) rather than enforcing a common function. Execution of the following command will produce a list of conflicts that should be examined by an annotator: potential_conflicts GenomeToBeAnnotated FileOfGenomesGivingContext ==== Step 5: Improvement of Annotation Via New Subsystems ==== Normal subsystem maintenance occurs constantly. The basic activity of our annotators is to extend existing subsystems and to define and populate new subsystems. These activities produce a gradual improvement in the quality of annotations for all genomes. All new annotations are logged as they are made. ==== Step 6: Continuous Refinement Via Analysis of Literature ==== Annotators should continuously review new literature, seeking cases in which gene functions can be improved based on new results. Sometimes, this results in improvements in function for a specific gene (and these results are then propagated to other members of the NMPDR pathogen class). More often, these new results are used as the basis for new subsystems and have a broader impact. e57bcea17932ea7f3500ea147916ea9536291996 1446 1445 2006-08-13T16:16:40Z FolkerMeyer 2 wikitext text/x-wiki == Annotation of Genomes: == === Standard Operating Procedure === === Introduction === This procedure describes the annotation process used by the SEED and NMPDR annotators and curators. Let us begin by discussing a number of terms that we use in this document: '''Functional Role''': The concept of functional role is both basic and primitive in the sense that we will not pretend to offer a precise definition. It corresponds roughly to a single logical role that a gene or gene product may play in the operation of a cell. Gene function: The function of a protein-encoding gene (PEG) is the functional role played by the product of the gene or an expression describing a set of roles played by the encoded protein. The operators used to construct expressions and the meanings associated with the operators are described in http://www.nmpdr.org/FIG/Html/SEED_functions.html Genes other than PEGs can also be assigned functions (e.g., SSU rRNA). However, in most cases the functions assigned to genes other than PEGs tend not to be problematic. This document will focus solely on annotation of PEGs. Assigning a gene function and annotation: Annotators assign gene functions to genes, and we call this process annotation. In most contexts, people use the term annotation to refer to assignments of function to the genes within a single organism. We certainly use the term in this sense, but we also use it to describe the process of assigning functions to corresponding genes from numerous genomes. Our basic approach to annotation is to ask our annotators to annotate the genes included in a subsystem (e.g., glycolysis) across all genomes. This process of annotation of the genes within a subsystem across a set of genomes, rather than annotation of genes within a single genome, allows our annotators to focus on a constrained set of functional roles and attempt to accurately identify exactly what variant, if any, of a subsystem exists in each of the genomes. We use the term annotation to refer to assigning functions to genes (either within a single organism or to a constrained set of gene/protein families across a set of organisms). This activity certainly is closely related to the construction of subsystems and protein families (which we call FIGfams), but we will describe those activities elsewhere. '''Subsystem''': A subsystem is a set of functional roles that an annotator has decided should be thought of as related. Frequently, subsystems represent the collection of functional roles that make up a metabolic pathway, a complex (e.g., the ribosome), or a class of proteins (e.g., two-component signal-transduction proteins within Staphylococcus aureus). A populated subsystem is a subsystem with an attached spreadsheet. The rows of the spreadsheet represent genomes and the columns represent the functional roles of the spreadsheet. Each cell contains the identifiers of genes from the corresponding genome the implement the specific functional role. That is, a populated subsystem specifies which genes implement instances of the subsystem in each of the genomes. The rows of a populated genome are assigned variant codes which describe which of a set of possible variants of the subsystem exist within each genome (special codes expressing a total absence of the subsystem or remaining uncertainty exist). Construction of a large set of curated populated subsystems is at the center of the NMPDR and SEED annotation efforts. '''FIGfam''': FIGfams are protein families generated by the Fellowship for Interpretation of Genomes (FIG). These families are based on the collection of subsystems, as well as correspondences between genes in closely related strains (we describe the construction of FIGfams in a separate SOP). The important properties of these families are as follows: # Two PEGs which both occur within a single FIGfam are believed to have the same function. # There is a decision procedure associated with the family which can be invoked to determine whether or not a gene can be “safely” assigned the function associated with the family. '''Metabolic Reconstruction''': When we use the term metabolic reconstruction of a given genome we will simply mean the set of populated subsystems that contain the genome, the PEGs (and their assigned functions) that are connected to functional roles in these populated subsystems, and the specific variant code associated with the genome in each of the populated subsystems. '''NMPDR pathogen genome''': The NMPDR is responsible for five classes of genomes: # Campylobacter jejuni # Listeria monocytogenes # Staphylococcus aureus # Streptococcus pneumoniae and Streptococcus pyogenes # Pathogenic Vibrio We refer to these genomes as the NMPDR pathogens. The NMPDR carefully annotates some close relatives of these classes to provide accurate comparative context. Similarly, it includes a diverse collection of complete genomes that it annotates less accurately to provide context for comparative analysis. Now we can discuss what we mean by the annotations and the standard procedure for making those annotations. === The Annotation Procedure === The annotation of genomes begins after the genes have been identified and the genome has been integrated into a SEED environment. The annotation process then proceeds through the following steps: # Use of FIGfams # Use of Subsystems # Annotation of Prophages # Resolution of Conflicts # Improvement of Annotation Via New Subsystems # Continuous Refinement Via Analysis of Literature The following sections cover each of these steps in detail. We present the sequence of steps as commands issued from the command line. In fact, we are constructing a pipeline managed from a web interface that is intended to allow a relatively unskilled user to control the process. ==== Step 1: Use of FIGfams ==== For each new genome, we form a set of anticipated families by gathering all FIGfams with members in genomes from the same class. We begin the annotation by taking the anticipated families and searching for occurrences of these FIGfams within the new genome. This is achieved by invoking install_anticipated_functions User GenomeToBeAnnotated FileOfGenomesGivingContext Where User is the individual issuing the command, GenomeToBeAnnotated is the ID of the genome to be annotated (it is assumed that this genome has already been installed in the current SEED), and FileOfGenomesGivingContext is a file containing genome IDs (one per line) of the existing genomes from the same class. The effect of running this command will be to locate the instances of families when possible, to assign the appropriate function to the located genes, and to record detailed annotations of which FIGfam families were used as the basis for each annotation (along with the User and timestamps). ==== Step 2: Use of Subsystems ==== Once initial assignments based on FIGfams has been accomplished, it is possible to rapidly assess the presence and absence of subsystems (it is worth noting that every functional role within existing subsystems is covered by a FIGfam). The process begins with potentially_missed_assignments GenomeToBeAnnotated FileOfGenomesGivingContext This command will produce a list of assignments that may have been missed. This list is formed by looking at subsystems contained in each of the genomes that make up the context, checking for subsystems in which a majority (but not all) of the genes have corresponding genes in the new genome, and candidates for the missing genes can be located. The tool produces a list of possibly missed assignments that must be checked by an annotator. Once the list of possibly missed assignments has been processed, the following command can be run: add_to_subsystems User GenomeToBeAnnotated FileOfGenomesGivingContext This command will compute the set of subsystems from the context genomes for which all of the corresponding genes can be located in the new genome. This set of subsystems will then be split into two lists: # Some of the subsystems are marked as automatically extendable by their curators. For these subsystems, the new genome will be added to the populated subsystem. # For those subsystems that are not marked as automatically extendable, the fact that the new genome should be added to the subsystem will be recorded. Curators for these subsystems will be notified and asked to add the new genome. The tentative metabolic reconstruction is formed (including subsystems from both lists). ==== Step 3: Annotation of Prophages and Mobil Elements ==== For each class of NMPDR pathogen we maintain as features a list of prophages and other mobil elements. Execution of mark_features prophage User GenomeToBeAnnotated FileOfGenomesGivingContext mark_features mobil_element User GenomeToBeAnnotated FileOfGenomesGivingContext will cause instances of these prohages and other mobile elements to be detected and marked as features in the new genome. These annotations will be logged. ==== Step 4: Resolution of Conflicts ==== FIGfams are not always annotated consistently. This can happen in cases in which it is possible to assert that a set of genes have a common function, but for which disagreement remains about exactly how to label the role played by members of the family. In such cases, a functional role is associated with the FIGfam, but individual members of the family may have distinct (inconsistent) functions. The number of such instances is gradually dropping, but we have adopted the position that it is better to retain the inconsistency (reflecting real uncertainty) rather than enforcing a common function. Execution of the following command will produce a list of conflicts that should be examined by an annotator: potential_conflicts GenomeToBeAnnotated FileOfGenomesGivingContext ==== Step 5: Improvement of Annotation Via New Subsystems ==== Normal subsystem maintenance occurs constantly. The basic activity of our annotators is to extend existing subsystems and to define and populate new subsystems. These activities produce a gradual improvement in the quality of annotations for all genomes. All new annotations are logged as they are made. ==== Step 6: Continuous Refinement Via Analysis of Literature ==== Annotators should continuously review new literature, seeking cases in which gene functions can be improved based on new results. Sometimes, this results in improvements in function for a specific gene (and these results are then propagated to other members of the NMPDR pathogen class). More often, these new results are used as the basis for new subsystems and have a broader impact. 2f0534d6c2bdd0a58eb5f013f30ba93a9f69e1c4 1447 1446 2006-08-13T16:17:25Z FolkerMeyer 2 wikitext text/x-wiki == Annotation of Genomes: == === Standard Operating Procedure === === Introduction === This procedure describes the annotation process used by the SEED and NMPDR annotators and curators. Let us begin by discussing a number of terms that we use in this document: '''Functional Role''': The concept of functional role is both basic and primitive in the sense that we will not pretend to offer a precise definition. It corresponds roughly to a single logical role that a gene or gene product may play in the operation of a cell. '''Gene function''': The function of a protein-encoding gene (PEG) is the functional role played by the product of the gene or an expression describing a set of roles played by the encoded protein. The operators used to construct expressions and the meanings associated with the operators are described in http://www.nmpdr.org/FIG/Html/SEED_functions.html Genes other than PEGs can also be assigned functions (e.g., SSU rRNA). However, in most cases the functions assigned to genes other than PEGs tend not to be problematic. This document will focus solely on annotation of PEGs. Assigning a gene function and annotation: Annotators assign gene functions to genes, and we call this process annotation. In most contexts, people use the term annotation to refer to assignments of function to the genes within a single organism. We certainly use the term in this sense, but we also use it to describe the process of assigning functions to corresponding genes from numerous genomes. Our basic approach to annotation is to ask our annotators to annotate the genes included in a subsystem (e.g., glycolysis) across all genomes. This process of annotation of the genes within a subsystem across a set of genomes, rather than annotation of genes within a single genome, allows our annotators to focus on a constrained set of functional roles and attempt to accurately identify exactly what variant, if any, of a subsystem exists in each of the genomes. We use the term annotation to refer to assigning functions to genes (either within a single organism or to a constrained set of gene/protein families across a set of organisms). This activity certainly is closely related to the construction of subsystems and protein families (which we call FIGfams), but we will describe those activities elsewhere. '''Subsystem''': A subsystem is a set of functional roles that an annotator has decided should be thought of as related. Frequently, subsystems represent the collection of functional roles that make up a metabolic pathway, a complex (e.g., the ribosome), or a class of proteins (e.g., two-component signal-transduction proteins within Staphylococcus aureus). A populated subsystem is a subsystem with an attached spreadsheet. The rows of the spreadsheet represent genomes and the columns represent the functional roles of the spreadsheet. Each cell contains the identifiers of genes from the corresponding genome the implement the specific functional role. That is, a populated subsystem specifies which genes implement instances of the subsystem in each of the genomes. The rows of a populated genome are assigned variant codes which describe which of a set of possible variants of the subsystem exist within each genome (special codes expressing a total absence of the subsystem or remaining uncertainty exist). Construction of a large set of curated populated subsystems is at the center of the NMPDR and SEED annotation efforts. '''FIGfam''': FIGfams are protein families generated by the Fellowship for Interpretation of Genomes (FIG). These families are based on the collection of subsystems, as well as correspondences between genes in closely related strains (we describe the construction of FIGfams in a separate SOP). The important properties of these families are as follows: # Two PEGs which both occur within a single FIGfam are believed to have the same function. # There is a decision procedure associated with the family which can be invoked to determine whether or not a gene can be “safely” assigned the function associated with the family. '''Metabolic Reconstruction''': When we use the term metabolic reconstruction of a given genome we will simply mean the set of populated subsystems that contain the genome, the PEGs (and their assigned functions) that are connected to functional roles in these populated subsystems, and the specific variant code associated with the genome in each of the populated subsystems. '''NMPDR pathogen genome''': The NMPDR is responsible for five classes of genomes: # Campylobacter jejuni # Listeria monocytogenes # Staphylococcus aureus # Streptococcus pneumoniae and Streptococcus pyogenes # Pathogenic Vibrio We refer to these genomes as the NMPDR pathogens. The NMPDR carefully annotates some close relatives of these classes to provide accurate comparative context. Similarly, it includes a diverse collection of complete genomes that it annotates less accurately to provide context for comparative analysis. Now we can discuss what we mean by the annotations and the standard procedure for making those annotations. === The Annotation Procedure === The annotation of genomes begins after the genes have been identified and the genome has been integrated into a SEED environment. The annotation process then proceeds through the following steps: # Use of FIGfams # Use of Subsystems # Annotation of Prophages # Resolution of Conflicts # Improvement of Annotation Via New Subsystems # Continuous Refinement Via Analysis of Literature The following sections cover each of these steps in detail. We present the sequence of steps as commands issued from the command line. In fact, we are constructing a pipeline managed from a web interface that is intended to allow a relatively unskilled user to control the process. ==== Step 1: Use of FIGfams ==== For each new genome, we form a set of anticipated families by gathering all FIGfams with members in genomes from the same class. We begin the annotation by taking the anticipated families and searching for occurrences of these FIGfams within the new genome. This is achieved by invoking install_anticipated_functions User GenomeToBeAnnotated FileOfGenomesGivingContext Where User is the individual issuing the command, GenomeToBeAnnotated is the ID of the genome to be annotated (it is assumed that this genome has already been installed in the current SEED), and FileOfGenomesGivingContext is a file containing genome IDs (one per line) of the existing genomes from the same class. The effect of running this command will be to locate the instances of families when possible, to assign the appropriate function to the located genes, and to record detailed annotations of which FIGfam families were used as the basis for each annotation (along with the User and timestamps). ==== Step 2: Use of Subsystems ==== Once initial assignments based on FIGfams has been accomplished, it is possible to rapidly assess the presence and absence of subsystems (it is worth noting that every functional role within existing subsystems is covered by a FIGfam). The process begins with potentially_missed_assignments GenomeToBeAnnotated FileOfGenomesGivingContext This command will produce a list of assignments that may have been missed. This list is formed by looking at subsystems contained in each of the genomes that make up the context, checking for subsystems in which a majority (but not all) of the genes have corresponding genes in the new genome, and candidates for the missing genes can be located. The tool produces a list of possibly missed assignments that must be checked by an annotator. Once the list of possibly missed assignments has been processed, the following command can be run: add_to_subsystems User GenomeToBeAnnotated FileOfGenomesGivingContext This command will compute the set of subsystems from the context genomes for which all of the corresponding genes can be located in the new genome. This set of subsystems will then be split into two lists: # Some of the subsystems are marked as automatically extendable by their curators. For these subsystems, the new genome will be added to the populated subsystem. # For those subsystems that are not marked as automatically extendable, the fact that the new genome should be added to the subsystem will be recorded. Curators for these subsystems will be notified and asked to add the new genome. The tentative metabolic reconstruction is formed (including subsystems from both lists). ==== Step 3: Annotation of Prophages and Mobil Elements ==== For each class of NMPDR pathogen we maintain as features a list of prophages and other mobil elements. Execution of mark_features prophage User GenomeToBeAnnotated FileOfGenomesGivingContext mark_features mobil_element User GenomeToBeAnnotated FileOfGenomesGivingContext will cause instances of these prohages and other mobile elements to be detected and marked as features in the new genome. These annotations will be logged. ==== Step 4: Resolution of Conflicts ==== FIGfams are not always annotated consistently. This can happen in cases in which it is possible to assert that a set of genes have a common function, but for which disagreement remains about exactly how to label the role played by members of the family. In such cases, a functional role is associated with the FIGfam, but individual members of the family may have distinct (inconsistent) functions. The number of such instances is gradually dropping, but we have adopted the position that it is better to retain the inconsistency (reflecting real uncertainty) rather than enforcing a common function. Execution of the following command will produce a list of conflicts that should be examined by an annotator: potential_conflicts GenomeToBeAnnotated FileOfGenomesGivingContext ==== Step 5: Improvement of Annotation Via New Subsystems ==== Normal subsystem maintenance occurs constantly. The basic activity of our annotators is to extend existing subsystems and to define and populate new subsystems. These activities produce a gradual improvement in the quality of annotations for all genomes. All new annotations are logged as they are made. ==== Step 6: Continuous Refinement Via Analysis of Literature ==== Annotators should continuously review new literature, seeking cases in which gene functions can be improved based on new results. Sometimes, this results in improvements in function for a specific gene (and these results are then propagated to other members of the NMPDR pathogen class). More often, these new results are used as the basis for new subsystems and have a broader impact. 1e695693d03896180dbaf6193dd1113edeac81ca 1451 1447 2006-08-13T16:30:58Z FolkerMeyer 2 wikitext text/x-wiki == Annotation of Genomes: == === Standard Operating Procedure === === Introduction === This procedure describes the annotation process used by the SEED and NMPDR annotators and curators. Let us begin by discussing a number of terms that we use in this document: '''Functional Role''': The concept of functional role is both basic and primitive in the sense that we will not pretend to offer a precise definition. It corresponds roughly to a single logical role that a gene or gene product may play in the operation of a cell. '''Gene function''': The function of a protein-encoding gene (PEG) is the functional role played by the product of the gene or an expression describing a set of roles played by the encoded protein. The operators used to construct expressions and the meanings associated with the operators are described in http://www.nmpdr.org/FIG/Html/SEED_functions.html Genes other than PEGs can also be assigned functions (e.g., SSU rRNA). However, in most cases the functions assigned to genes other than PEGs tend not to be problematic. This document will focus solely on annotation of PEGs. '''Assigning a gene function and annotation''': Annotators assign gene functions to genes, and we call this process annotation. In most contexts, people use the term annotation to refer to assignments of function to the genes within a single organism. We certainly use the term in this sense, but we also use it to describe the process of assigning functions to corresponding genes from numerous genomes. Our basic approach to annotation is to ask our annotators to annotate the genes included in a subsystem (e.g., glycolysis) across all genomes. This process of annotation of the genes within a subsystem across a set of genomes, rather than annotation of genes within a single genome, allows our annotators to focus on a constrained set of functional roles and attempt to accurately identify exactly what variant, if any, of a subsystem exists in each of the genomes. We use the term annotation to refer to assigning functions to genes (either within a single organism or to a constrained set of gene/protein families across a set of organisms). This activity certainly is closely related to the construction of subsystems and protein families (which we call FIGfams), but we will describe those activities elsewhere. '''Subsystem''': A subsystem is a set of functional roles that an annotator has decided should be thought of as related. Frequently, subsystems represent the collection of functional roles that make up a metabolic pathway, a complex (e.g., the ribosome), or a class of proteins (e.g., two-component signal-transduction proteins within Staphylococcus aureus). A populated subsystem is a subsystem with an attached spreadsheet. The rows of the spreadsheet represent genomes and the columns represent the functional roles of the spreadsheet. Each cell contains the identifiers of genes from the corresponding genome the implement the specific functional role. That is, a populated subsystem specifies which genes implement instances of the subsystem in each of the genomes. The rows of a populated genome are assigned variant codes which describe which of a set of possible variants of the subsystem exist within each genome (special codes expressing a total absence of the subsystem or remaining uncertainty exist). Construction of a large set of curated populated subsystems is at the center of the NMPDR and SEED annotation efforts. '''FIGfam''': FIGfams are protein families generated by the Fellowship for Interpretation of Genomes (FIG). These families are based on the collection of subsystems, as well as correspondences between genes in closely related strains (we describe the construction of FIGfams in a separate SOP). The important properties of these families are as follows: # Two PEGs which both occur within a single FIGfam are believed to have the same function. # There is a decision procedure associated with the family which can be invoked to determine whether or not a gene can be “safely” assigned the function associated with the family. '''Metabolic Reconstruction''': When we use the term metabolic reconstruction of a given genome we will simply mean the set of populated subsystems that contain the genome, the PEGs (and their assigned functions) that are connected to functional roles in these populated subsystems, and the specific variant code associated with the genome in each of the populated subsystems. '''NMPDR pathogen genome''': The NMPDR is responsible for five classes of genomes: # Campylobacter jejuni # Listeria monocytogenes # Staphylococcus aureus # Streptococcus pneumoniae and Streptococcus pyogenes # Pathogenic Vibrio We refer to these genomes as the NMPDR pathogens. The NMPDR carefully annotates some close relatives of these classes to provide accurate comparative context. Similarly, it includes a diverse collection of complete genomes that it annotates less accurately to provide context for comparative analysis. Now we can discuss what we mean by the annotations and the standard procedure for making those annotations. === The Annotation Procedure === The annotation of genomes begins after the genes have been identified and the genome has been integrated into a SEED environment. The annotation process then proceeds through the following steps: # Use of FIGfams # Use of Subsystems # Annotation of Prophages # Resolution of Conflicts # Improvement of Annotation Via New Subsystems # Continuous Refinement Via Analysis of Literature The following sections cover each of these steps in detail. We present the sequence of steps as commands issued from the command line. In fact, we are constructing a pipeline managed from a web interface that is intended to allow a relatively unskilled user to control the process. ==== Step 1: Use of FIGfams ==== For each new genome, we form a set of anticipated families by gathering all FIGfams with members in genomes from the same class. We begin the annotation by taking the anticipated families and searching for occurrences of these FIGfams within the new genome. This is achieved by invoking install_anticipated_functions User GenomeToBeAnnotated FileOfGenomesGivingContext Where User is the individual issuing the command, GenomeToBeAnnotated is the ID of the genome to be annotated (it is assumed that this genome has already been installed in the current SEED), and FileOfGenomesGivingContext is a file containing genome IDs (one per line) of the existing genomes from the same class. The effect of running this command will be to locate the instances of families when possible, to assign the appropriate function to the located genes, and to record detailed annotations of which FIGfam families were used as the basis for each annotation (along with the User and timestamps). ==== Step 2: Use of Subsystems ==== Once initial assignments based on FIGfams has been accomplished, it is possible to rapidly assess the presence and absence of subsystems (it is worth noting that every functional role within existing subsystems is covered by a FIGfam). The process begins with potentially_missed_assignments GenomeToBeAnnotated FileOfGenomesGivingContext This command will produce a list of assignments that may have been missed. This list is formed by looking at subsystems contained in each of the genomes that make up the context, checking for subsystems in which a majority (but not all) of the genes have corresponding genes in the new genome, and candidates for the missing genes can be located. The tool produces a list of possibly missed assignments that must be checked by an annotator. Once the list of possibly missed assignments has been processed, the following command can be run: add_to_subsystems User GenomeToBeAnnotated FileOfGenomesGivingContext This command will compute the set of subsystems from the context genomes for which all of the corresponding genes can be located in the new genome. This set of subsystems will then be split into two lists: # Some of the subsystems are marked as automatically extendable by their curators. For these subsystems, the new genome will be added to the populated subsystem. # For those subsystems that are not marked as automatically extendable, the fact that the new genome should be added to the subsystem will be recorded. Curators for these subsystems will be notified and asked to add the new genome. The tentative metabolic reconstruction is formed (including subsystems from both lists). ==== Step 3: Annotation of Prophages and Mobil Elements ==== For each class of NMPDR pathogen we maintain as features a list of prophages and other mobil elements. Execution of mark_features prophage User GenomeToBeAnnotated FileOfGenomesGivingContext mark_features mobil_element User GenomeToBeAnnotated FileOfGenomesGivingContext will cause instances of these prohages and other mobile elements to be detected and marked as features in the new genome. These annotations will be logged. ==== Step 4: Resolution of Conflicts ==== FIGfams are not always annotated consistently. This can happen in cases in which it is possible to assert that a set of genes have a common function, but for which disagreement remains about exactly how to label the role played by members of the family. In such cases, a functional role is associated with the FIGfam, but individual members of the family may have distinct (inconsistent) functions. The number of such instances is gradually dropping, but we have adopted the position that it is better to retain the inconsistency (reflecting real uncertainty) rather than enforcing a common function. Execution of the following command will produce a list of conflicts that should be examined by an annotator: potential_conflicts GenomeToBeAnnotated FileOfGenomesGivingContext ==== Step 5: Improvement of Annotation Via New Subsystems ==== Normal subsystem maintenance occurs constantly. The basic activity of our annotators is to extend existing subsystems and to define and populate new subsystems. These activities produce a gradual improvement in the quality of annotations for all genomes. All new annotations are logged as they are made. ==== Step 6: Continuous Refinement Via Analysis of Literature ==== Annotators should continuously review new literature, seeking cases in which gene functions can be improved based on new results. Sometimes, this results in improvements in function for a specific gene (and these results are then propagated to other members of the NMPDR pathogen class). More often, these new results are used as the basis for new subsystems and have a broader impact. c3f99926f85ab981bdd3998caa567334004051e7 1463 1451 2006-08-13T23:08:42Z VeronikaVonstein 6 [[Annotation]] moved to [[Annotation of close strains]] wikitext text/x-wiki == Annotation of Genomes: == === Standard Operating Procedure === === Introduction === This procedure describes the annotation process used by the SEED and NMPDR annotators and curators. Let us begin by discussing a number of terms that we use in this document: '''Functional Role''': The concept of functional role is both basic and primitive in the sense that we will not pretend to offer a precise definition. It corresponds roughly to a single logical role that a gene or gene product may play in the operation of a cell. '''Gene function''': The function of a protein-encoding gene (PEG) is the functional role played by the product of the gene or an expression describing a set of roles played by the encoded protein. The operators used to construct expressions and the meanings associated with the operators are described in http://www.nmpdr.org/FIG/Html/SEED_functions.html Genes other than PEGs can also be assigned functions (e.g., SSU rRNA). However, in most cases the functions assigned to genes other than PEGs tend not to be problematic. This document will focus solely on annotation of PEGs. '''Assigning a gene function and annotation''': Annotators assign gene functions to genes, and we call this process annotation. In most contexts, people use the term annotation to refer to assignments of function to the genes within a single organism. We certainly use the term in this sense, but we also use it to describe the process of assigning functions to corresponding genes from numerous genomes. Our basic approach to annotation is to ask our annotators to annotate the genes included in a subsystem (e.g., glycolysis) across all genomes. This process of annotation of the genes within a subsystem across a set of genomes, rather than annotation of genes within a single genome, allows our annotators to focus on a constrained set of functional roles and attempt to accurately identify exactly what variant, if any, of a subsystem exists in each of the genomes. We use the term annotation to refer to assigning functions to genes (either within a single organism or to a constrained set of gene/protein families across a set of organisms). This activity certainly is closely related to the construction of subsystems and protein families (which we call FIGfams), but we will describe those activities elsewhere. '''Subsystem''': A subsystem is a set of functional roles that an annotator has decided should be thought of as related. Frequently, subsystems represent the collection of functional roles that make up a metabolic pathway, a complex (e.g., the ribosome), or a class of proteins (e.g., two-component signal-transduction proteins within Staphylococcus aureus). A populated subsystem is a subsystem with an attached spreadsheet. The rows of the spreadsheet represent genomes and the columns represent the functional roles of the spreadsheet. Each cell contains the identifiers of genes from the corresponding genome the implement the specific functional role. That is, a populated subsystem specifies which genes implement instances of the subsystem in each of the genomes. The rows of a populated genome are assigned variant codes which describe which of a set of possible variants of the subsystem exist within each genome (special codes expressing a total absence of the subsystem or remaining uncertainty exist). Construction of a large set of curated populated subsystems is at the center of the NMPDR and SEED annotation efforts. '''FIGfam''': FIGfams are protein families generated by the Fellowship for Interpretation of Genomes (FIG). These families are based on the collection of subsystems, as well as correspondences between genes in closely related strains (we describe the construction of FIGfams in a separate SOP). The important properties of these families are as follows: # Two PEGs which both occur within a single FIGfam are believed to have the same function. # There is a decision procedure associated with the family which can be invoked to determine whether or not a gene can be “safely” assigned the function associated with the family. '''Metabolic Reconstruction''': When we use the term metabolic reconstruction of a given genome we will simply mean the set of populated subsystems that contain the genome, the PEGs (and their assigned functions) that are connected to functional roles in these populated subsystems, and the specific variant code associated with the genome in each of the populated subsystems. '''NMPDR pathogen genome''': The NMPDR is responsible for five classes of genomes: # Campylobacter jejuni # Listeria monocytogenes # Staphylococcus aureus # Streptococcus pneumoniae and Streptococcus pyogenes # Pathogenic Vibrio We refer to these genomes as the NMPDR pathogens. The NMPDR carefully annotates some close relatives of these classes to provide accurate comparative context. Similarly, it includes a diverse collection of complete genomes that it annotates less accurately to provide context for comparative analysis. Now we can discuss what we mean by the annotations and the standard procedure for making those annotations. === The Annotation Procedure === The annotation of genomes begins after the genes have been identified and the genome has been integrated into a SEED environment. The annotation process then proceeds through the following steps: # Use of FIGfams # Use of Subsystems # Annotation of Prophages # Resolution of Conflicts # Improvement of Annotation Via New Subsystems # Continuous Refinement Via Analysis of Literature The following sections cover each of these steps in detail. We present the sequence of steps as commands issued from the command line. In fact, we are constructing a pipeline managed from a web interface that is intended to allow a relatively unskilled user to control the process. ==== Step 1: Use of FIGfams ==== For each new genome, we form a set of anticipated families by gathering all FIGfams with members in genomes from the same class. We begin the annotation by taking the anticipated families and searching for occurrences of these FIGfams within the new genome. This is achieved by invoking install_anticipated_functions User GenomeToBeAnnotated FileOfGenomesGivingContext Where User is the individual issuing the command, GenomeToBeAnnotated is the ID of the genome to be annotated (it is assumed that this genome has already been installed in the current SEED), and FileOfGenomesGivingContext is a file containing genome IDs (one per line) of the existing genomes from the same class. The effect of running this command will be to locate the instances of families when possible, to assign the appropriate function to the located genes, and to record detailed annotations of which FIGfam families were used as the basis for each annotation (along with the User and timestamps). ==== Step 2: Use of Subsystems ==== Once initial assignments based on FIGfams has been accomplished, it is possible to rapidly assess the presence and absence of subsystems (it is worth noting that every functional role within existing subsystems is covered by a FIGfam). The process begins with potentially_missed_assignments GenomeToBeAnnotated FileOfGenomesGivingContext This command will produce a list of assignments that may have been missed. This list is formed by looking at subsystems contained in each of the genomes that make up the context, checking for subsystems in which a majority (but not all) of the genes have corresponding genes in the new genome, and candidates for the missing genes can be located. The tool produces a list of possibly missed assignments that must be checked by an annotator. Once the list of possibly missed assignments has been processed, the following command can be run: add_to_subsystems User GenomeToBeAnnotated FileOfGenomesGivingContext This command will compute the set of subsystems from the context genomes for which all of the corresponding genes can be located in the new genome. This set of subsystems will then be split into two lists: # Some of the subsystems are marked as automatically extendable by their curators. For these subsystems, the new genome will be added to the populated subsystem. # For those subsystems that are not marked as automatically extendable, the fact that the new genome should be added to the subsystem will be recorded. Curators for these subsystems will be notified and asked to add the new genome. The tentative metabolic reconstruction is formed (including subsystems from both lists). ==== Step 3: Annotation of Prophages and Mobil Elements ==== For each class of NMPDR pathogen we maintain as features a list of prophages and other mobil elements. Execution of mark_features prophage User GenomeToBeAnnotated FileOfGenomesGivingContext mark_features mobil_element User GenomeToBeAnnotated FileOfGenomesGivingContext will cause instances of these prohages and other mobile elements to be detected and marked as features in the new genome. These annotations will be logged. ==== Step 4: Resolution of Conflicts ==== FIGfams are not always annotated consistently. This can happen in cases in which it is possible to assert that a set of genes have a common function, but for which disagreement remains about exactly how to label the role played by members of the family. In such cases, a functional role is associated with the FIGfam, but individual members of the family may have distinct (inconsistent) functions. The number of such instances is gradually dropping, but we have adopted the position that it is better to retain the inconsistency (reflecting real uncertainty) rather than enforcing a common function. Execution of the following command will produce a list of conflicts that should be examined by an annotator: potential_conflicts GenomeToBeAnnotated FileOfGenomesGivingContext ==== Step 5: Improvement of Annotation Via New Subsystems ==== Normal subsystem maintenance occurs constantly. The basic activity of our annotators is to extend existing subsystems and to define and populate new subsystems. These activities produce a gradual improvement in the quality of annotations for all genomes. All new annotations are logged as they are made. ==== Step 6: Continuous Refinement Via Analysis of Literature ==== Annotators should continuously review new literature, seeking cases in which gene functions can be improved based on new results. Sometimes, this results in improvements in function for a specific gene (and these results are then propagated to other members of the NMPDR pathogen class). More often, these new results are used as the basis for new subsystems and have a broader impact. c3f99926f85ab981bdd3998caa567334004051e7 0 1367 1448 1386 2006-08-13T16:25:01Z FolkerMeyer 2 wikitext text/x-wiki === Annotators SEED === The master copy for all data in the SEED environment. Users can not access this password protected site. === Annotation === Annotation can be defined as assigning a gene function to a specific sequence. Traditionally annotation has been performed on a gene by gene basis in each genome separately. The SEED approach is based on the idea to annotate many genomes at a time. The SEED approach to annotation requires subsystems to be created, see [[#Clearinghouse]]. === FIGfam === FIGfams are protein families generated by the Fellowship for Interpretation of Genomes (FIG). These families are based on the collection of subsystems, as well as correspondences between genes in closely related strains (we describe the construction of FIGfams in a separate SOP). The important properties of these families are as follows: # Two PEGs which both occur within a single FIGfam are believed to have the same function. # There is a decision procedure associated with the family which can be invoked to determine whether or not a gene can be “safely” assigned the function associated with the family. === Functional role === The concept of functional role is both basic and primitive in the sense that we will not pretend to offer a precise definition. It corresponds roughly to a single logical role that a gene or gene product may play in the operation of a cell. === Gene function === The function of a protein-encoding gene (PEG) is the functional role played by the product of the gene or an expression describing a set of roles played by the encoded protein. The operators used to construct expressions and the meanings associated with the operators are described in http://www.nmpdr.org/FIG/Html/SEED_functions.html Genes other than PEGs can also be assigned functions (e.g., SSU rRNA). However, in most cases the functions assigned to genes other than PEGs tend not to be problematic. This document will focus solely on annotation of PEGs. Assigning a gene function and annotation: Annotators assign gene functions to genes, and we call this process annotation. In most contexts, people use the term annotation to refer to assignments of function to the genes within a single organism. We certainly use the term in this sense, but we also use it to describe the process of assigning functions to corresponding genes from numerous genomes. Our basic approach to annotation is to ask our annotators to annotate the genes included in a subsystem (e.g., glycolysis) across all genomes. This process of annotation of the genes within a subsystem across a set of genomes, rather than annotation of genes within a single genome, allows our annotators to focus on a constrained set of functional roles and attempt to accurately identify exactly what variant, if any, of a subsystem exists in each of the genomes. We use the term annotation to refer to assigning functions to genes (either within a single organism or to a constrained set of gene/protein families across a set of organisms). This activity certainly is closely related to the construction of subsystems and protein families (which we call FIGfams), but we will describe those activities elsewhere. === Metabolic Reconstruction When we use the term metabolic reconstruction of a given genome we will simply mean the set of populated subsystems that contain the genome, the PEGs (and their assigned functions) that are connected to functional roles in these populated subsystems, and the specific variant code associated with the genome in each of the populated subsystems. === NMPDR pathogen genome ===: The NMPDR is responsible for five classes of genomes: # Campylobacter jejuni # Listeria monocytogenes # Staphylococcus aureus # Streptococcus pneumoniae and Streptococcus pyogenes # Pathogenic Vibrio === PEG === A Protein Encoding Gene (PEG) is equivalent to a CDS (Coding Sequence). === Subsystem === A subsystem is a set of functional roles that an annotator has decided should be thought of as related. Frequently, subsystems represent the collection of functional roles that make up a metabolic pathway, a complex (e.g., the ribosome), or a class of proteins (e.g., two-component signal-transduction proteins within Staphylococcus aureus). A populated subsystem is a subsystem with an attached spreadsheet. The rows of the spreadsheet represent genomes and the columns represent the functional roles of the spreadsheet. Each cell contains the identifiers of genes from the corresponding genome the implement the specific functional role. That is, a populated subsystem specifies which genes implement instances of the subsystem in each of the genomes. The rows of a populated genome are assigned variant codes which describe which of a set of possible variants of the subsystem exist within each genome (special codes expressing a total absence of the subsystem or remaining uncertainty exist). Construction of a large set of curated populated subsystems is at the center of the NMPDR and SEED annotation efforts. === Subsystem Clearing House === Since annotators can work on any machine (including the public SEED) the way to propagate subsystems is via [http://anno-2.nmpdr.org/FIG/p2p/ch.cgi Subsystem Clearing House web page]. ===SEED etymology=== 399c59ada094690f67d7bc95c11135a170735d7b 1449 1448 2006-08-13T16:28:55Z FolkerMeyer 2 wikitext text/x-wiki === Annotators SEED === The master copy for all data in the SEED environment. Users can not access this password protected site. === Annotation === Annotation can be defined as assigning a gene function to a specific sequence. Traditionally annotation has been performed on a gene by gene basis in each genome separately. The SEED approach is based on the idea to annotate many genomes at a time. The SEED approach to annotation requires subsystems to be created, see [[#Clearinghouse]]. === Assigning a gene function and annotation === Annotators assign gene functions to genes, and we call this process annotation. In most contexts, people use the term annotation to refer to assignments of function to the genes within a single organism. We certainly use the term in this sense, but we also use it to describe the process of assigning functions to corresponding genes from numerous genomes. Our basic approach to annotation is to ask our annotators to annotate the genes included in a [[#subsystem]] (e.g., glycolysis) across all genomes. This process of annotation of the genes within a subsystem across a set of genomes, rather than annotation of genes within a single genome, allows our annotators to focus on a constrained set of functional roles and attempt to accurately identify exactly what variant, if any, of a subsystem exists in each of the genomes. We use the term annotation to refer to assigning functions to genes (either within a single organism or to a constrained set of gene/protein families across a set of organisms). This activity certainly is closely related to the construction of subsystems and protein families (which we call FIGfams), but we will describe those activities elsewhere. === Assignment === please see [[#Assigning_a_gene_function_and_annotation]] === FIGfam === FIGfams are protein families generated by the Fellowship for Interpretation of Genomes (FIG). These families are based on the collection of subsystems, as well as correspondences between genes in closely related strains (we describe the construction of FIGfams in a separate SOP). The important properties of these families are as follows: # Two PEGs which both occur within a single FIGfam are believed to have the same function. # There is a decision procedure associated with the family which can be invoked to determine whether or not a gene can be “safely” assigned the function associated with the family. === Functional role === The concept of functional role is both basic and primitive in the sense that we will not pretend to offer a precise definition. It corresponds roughly to a single logical role that a gene or gene product may play in the operation of a cell. === Gene function === The function of a protein-encoding gene (PEG) is the functional role played by the product of the gene or an expression describing a set of roles played by the encoded protein. The operators used to construct expressions and the meanings associated with the operators are described in http://www.nmpdr.org/FIG/Html/SEED_functions.html Genes other than PEGs can also be assigned functions (e.g., SSU rRNA). However, in most cases the functions assigned to genes other than PEGs tend not to be problematic. This document will focus solely on annotation of PEGs. === Metabolic Reconstruction When we use the term metabolic reconstruction of a given genome we will simply mean the set of populated subsystems that contain the genome, the PEGs (and their assigned functions) that are connected to functional roles in these populated subsystems, and the specific variant code associated with the genome in each of the populated subsystems. === NMPDR pathogen genome ===: The NMPDR is responsible for five classes of genomes: # Campylobacter jejuni # Listeria monocytogenes # Staphylococcus aureus # Streptococcus pneumoniae and Streptococcus pyogenes # Pathogenic Vibrio === PEG === A Protein Encoding Gene (PEG) is equivalent to a CDS (Coding Sequence). === Subsystem === A subsystem is a set of functional roles that an annotator has decided should be thought of as related. Frequently, subsystems represent the collection of functional roles that make up a metabolic pathway, a complex (e.g., the ribosome), or a class of proteins (e.g., two-component signal-transduction proteins within Staphylococcus aureus). A populated subsystem is a subsystem with an attached spreadsheet. The rows of the spreadsheet represent genomes and the columns represent the functional roles of the spreadsheet. Each cell contains the identifiers of genes from the corresponding genome the implement the specific functional role. That is, a populated subsystem specifies which genes implement instances of the subsystem in each of the genomes. The rows of a populated genome are assigned variant codes which describe which of a set of possible variants of the subsystem exist within each genome (special codes expressing a total absence of the subsystem or remaining uncertainty exist). Construction of a large set of curated populated subsystems is at the center of the NMPDR and SEED annotation efforts. === Subsystem Clearing House === Since annotators can work on any machine (including the public SEED) the way to propagate subsystems is via [http://anno-2.nmpdr.org/FIG/p2p/ch.cgi Subsystem Clearing House web page]. ===SEED etymology=== 033e72ab9656bfe0eecd2a7bfd5efa92e72cb0d9 1450 1449 2006-08-13T16:30:42Z FolkerMeyer 2 wikitext text/x-wiki === Annotators SEED === The master copy for all data in the SEED environment. Users can not access this password protected site. === Annotation === Annotation can be defined as assigning a gene function to a specific sequence. Traditionally annotation has been performed on a gene by gene basis in each genome separately. The SEED approach is based on the idea to annotate many genomes at a time. The SEED approach to annotation requires subsystems to be created, see [[#Clearinghouse|Clearinghouse]]. === Assigning a gene function and annotation === Annotators assign gene functions to genes, and we call this process annotation. In most contexts, people use the term annotation to refer to assignments of function to the genes within a single organism. We certainly use the term in this sense, but we also use it to describe the process of assigning functions to corresponding genes from numerous genomes. Our basic approach to annotation is to ask our annotators to annotate the genes included in a [[#subsystem]] (e.g., glycolysis) across all genomes. This process of annotation of the genes within a subsystem across a set of genomes, rather than annotation of genes within a single genome, allows our annotators to focus on a constrained set of functional roles and attempt to accurately identify exactly what variant, if any, of a subsystem exists in each of the genomes. We use the term annotation to refer to assigning functions to genes (either within a single organism or to a constrained set of gene/protein families across a set of organisms). This activity certainly is closely related to the construction of subsystems and protein families (which we call FIGfams), but we will describe those activities elsewhere. === Assignment === please see [[#Assigning_a_gene_function_and_annotation| Assigning a gene function and annotation]] === FIGfam === FIGfams are protein families generated by the Fellowship for Interpretation of Genomes (FIG). These families are based on the collection of subsystems, as well as correspondences between genes in closely related strains (we describe the construction of FIGfams in a separate SOP). The important properties of these families are as follows: # Two PEGs which both occur within a single FIGfam are believed to have the same function. # There is a decision procedure associated with the family which can be invoked to determine whether or not a gene can be “safely” assigned the function associated with the family. === Functional role === The concept of functional role is both basic and primitive in the sense that we will not pretend to offer a precise definition. It corresponds roughly to a single logical role that a gene or gene product may play in the operation of a cell. === Gene function === The function of a protein-encoding gene (PEG) is the functional role played by the product of the gene or an expression describing a set of roles played by the encoded protein. The operators used to construct expressions and the meanings associated with the operators are described in http://www.nmpdr.org/FIG/Html/SEED_functions.html Genes other than PEGs can also be assigned functions (e.g., SSU rRNA). However, in most cases the functions assigned to genes other than PEGs tend not to be problematic. This document will focus solely on annotation of PEGs. === Metabolic Reconstruction When we use the term metabolic reconstruction of a given genome we will simply mean the set of populated subsystems that contain the genome, the PEGs (and their assigned functions) that are connected to functional roles in these populated subsystems, and the specific variant code associated with the genome in each of the populated subsystems. === NMPDR pathogen genome ===: The NMPDR is responsible for five classes of genomes: # Campylobacter jejuni # Listeria monocytogenes # Staphylococcus aureus # Streptococcus pneumoniae and Streptococcus pyogenes # Pathogenic Vibrio === PEG === A Protein Encoding Gene (PEG) is equivalent to a CDS (Coding Sequence). === Subsystem === A subsystem is a set of functional roles that an annotator has decided should be thought of as related. Frequently, subsystems represent the collection of functional roles that make up a metabolic pathway, a complex (e.g., the ribosome), or a class of proteins (e.g., two-component signal-transduction proteins within Staphylococcus aureus). A populated subsystem is a subsystem with an attached spreadsheet. The rows of the spreadsheet represent genomes and the columns represent the functional roles of the spreadsheet. Each cell contains the identifiers of genes from the corresponding genome the implement the specific functional role. That is, a populated subsystem specifies which genes implement instances of the subsystem in each of the genomes. The rows of a populated genome are assigned variant codes which describe which of a set of possible variants of the subsystem exist within each genome (special codes expressing a total absence of the subsystem or remaining uncertainty exist). Construction of a large set of curated populated subsystems is at the center of the NMPDR and SEED annotation efforts. === Subsystem Clearing House === Since annotators can work on any machine (including the public SEED) the way to propagate subsystems is via [http://anno-2.nmpdr.org/FIG/p2p/ch.cgi Subsystem Clearing House web page]. ===SEED etymology=== 517ebd4db3c6f52ae8475943bdffdae1a76875eb 1452 1450 2006-08-13T16:33:42Z FolkerMeyer 2 wikitext text/x-wiki === Annotators SEED === The master copy for all data in the SEED environment. Users can not access this password protected site. === Annotation === please see [[#Assigning_a_gene_function_and_annotation| Assigning a gene function and annotation]] === Assigning a gene function and annotation === Annotators assign gene functions to genes, and we call this process annotation. In most contexts, people use the term annotation to refer to assignments of function to the genes within a single organism. We certainly use the term in this sense, but we also use it to describe the process of assigning functions to corresponding genes from numerous genomes. Our basic approach to annotation is to ask our annotators to annotate the genes included in a [[#subsystem]] (e.g., glycolysis) across all genomes. This process of annotation of the genes within a subsystem across a set of genomes, rather than annotation of genes within a single genome, allows our annotators to focus on a constrained set of functional roles and attempt to accurately identify exactly what variant, if any, of a subsystem exists in each of the genomes. We use the term annotation to refer to assigning functions to genes (either within a single organism or to a constrained set of gene/protein families across a set of organisms). This activity certainly is closely related to the construction of subsystems and protein families (which we call FIGfams), but we will describe those activities elsewhere. === Assignment === please see [[#Assigning_a_gene_function_and_annotation| Assigning a gene function and annotation]] == Clearinghouse === please see [[#SubsystemClearinghouse|Subsystem Clearinghouse]] === FIGfam === FIGfams are protein families generated by the Fellowship for Interpretation of Genomes (FIG). These families are based on the collection of subsystems, as well as correspondences between genes in closely related strains (we describe the construction of FIGfams in a separate SOP). The important properties of these families are as follows: # Two PEGs which both occur within a single FIGfam are believed to have the same function. # There is a decision procedure associated with the family which can be invoked to determine whether or not a gene can be “safely” assigned the function associated with the family. === Functional role === The concept of functional role is both basic and primitive in the sense that we will not pretend to offer a precise definition. It corresponds roughly to a single logical role that a gene or gene product may play in the operation of a cell. === Gene function === The function of a protein-encoding gene (PEG) is the functional role played by the product of the gene or an expression describing a set of roles played by the encoded protein. The operators used to construct expressions and the meanings associated with the operators are described in http://www.nmpdr.org/FIG/Html/SEED_functions.html Genes other than PEGs can also be assigned functions (e.g., SSU rRNA). However, in most cases the functions assigned to genes other than PEGs tend not to be problematic. This document will focus solely on annotation of PEGs. === Metabolic Reconstruction When we use the term metabolic reconstruction of a given genome we will simply mean the set of populated subsystems that contain the genome, the PEGs (and their assigned functions) that are connected to functional roles in these populated subsystems, and the specific variant code associated with the genome in each of the populated subsystems. === NMPDR pathogen genome ===: The NMPDR is responsible for five classes of genomes: # Campylobacter jejuni # Listeria monocytogenes # Staphylococcus aureus # Streptococcus pneumoniae and Streptococcus pyogenes # Pathogenic Vibrio === PEG === A Protein Encoding Gene (PEG) is equivalent to a CDS (Coding Sequence). === Subsystem === A subsystem is a set of functional roles that an annotator has decided should be thought of as related. Frequently, subsystems represent the collection of functional roles that make up a metabolic pathway, a complex (e.g., the ribosome), or a class of proteins (e.g., two-component signal-transduction proteins within Staphylococcus aureus). A populated subsystem is a subsystem with an attached spreadsheet. The rows of the spreadsheet represent genomes and the columns represent the functional roles of the spreadsheet. Each cell contains the identifiers of genes from the corresponding genome the implement the specific functional role. That is, a populated subsystem specifies which genes implement instances of the subsystem in each of the genomes. The rows of a populated genome are assigned variant codes which describe which of a set of possible variants of the subsystem exist within each genome (special codes expressing a total absence of the subsystem or remaining uncertainty exist). Construction of a large set of curated populated subsystems is at the center of the NMPDR and SEED annotation efforts. === Subsystem Clearing House === Since annotators can work on any machine (including the public SEED) the way to propagate subsystems is via [http://anno-2.nmpdr.org/FIG/p2p/ch.cgi Subsystem Clearing House web page]. ===SEED etymology=== be6a64bdfcab5b2bcc4dc7be41d6ea8658d49199 1453 1452 2006-08-13T16:35:57Z FolkerMeyer 2 wikitext text/x-wiki === Annotators SEED === The master copy for all data in the SEED environment. Users can not access this password protected site. === Annotation === please see [[#Assigning_a_gene_function_and_annotation| Assigning a gene function and annotation]] === Assigning a gene function and annotation === Annotators assign gene functions to genes, and we call this process annotation. In most contexts, people use the term annotation to refer to assignments of function to the genes within a single organism. We certainly use the term in this sense, but we also use it to describe the process of assigning functions to corresponding genes from numerous genomes. Our basic approach to annotation is to ask our annotators to annotate the genes included in a [[#subsystem]] (e.g., glycolysis) across all genomes. This process of annotation of the genes within a subsystem across a set of genomes, rather than annotation of genes within a single genome, allows our annotators to focus on a constrained set of functional roles and attempt to accurately identify exactly what variant, if any, of a subsystem exists in each of the genomes. We use the term annotation to refer to assigning functions to genes (either within a single organism or to a constrained set of gene/protein families across a set of organisms). This activity certainly is closely related to the construction of subsystems and protein families (which we call FIGfams), but we will describe those activities elsewhere. === Assignment === please see [[#Assigning_a_gene_function_and_annotation| Assigning a gene function and annotation]] === Clearinghouse === please see [[#SubsystemClearinghouse|Subsystem Clearinghouse]] === FIGfam === FIGfams are protein families generated by the Fellowship for Interpretation of Genomes (FIG). These families are based on the collection of subsystems, as well as correspondences between genes in closely related strains (we describe the construction of FIGfams in a separate SOP). The important properties of these families are as follows: # Two PEGs which both occur within a single FIGfam are believed to have the same function. # There is a decision procedure associated with the family which can be invoked to determine whether or not a gene can be “safely” assigned the function associated with the family. === Functional role === The concept of functional role is both basic and primitive in the sense that we will not pretend to offer a precise definition. It corresponds roughly to a single logical role that a gene or gene product may play in the operation of a cell. === Gene function === The function of a protein-encoding gene (PEG) is the functional role played by the product of the gene or an expression describing a set of roles played by the encoded protein. The operators used to construct expressions and the meanings associated with the operators are described in http://www.nmpdr.org/FIG/Html/SEED_functions.html Genes other than PEGs can also be assigned functions (e.g., SSU rRNA). However, in most cases the functions assigned to genes other than PEGs tend not to be problematic. This document will focus solely on annotation of PEGs. === Metabolic Reconstruction When we use the term metabolic reconstruction of a given genome we will simply mean the set of populated subsystems that contain the genome, the PEGs (and their assigned functions) that are connected to functional roles in these populated subsystems, and the specific variant code associated with the genome in each of the populated subsystems. === NMPDR pathogen genome ===: The NMPDR is responsible for five classes of genomes: # Campylobacter jejuni # Listeria monocytogenes # Staphylococcus aureus # Streptococcus pneumoniae and Streptococcus pyogenes # Pathogenic Vibrio === PEG === A Protein Encoding Gene (PEG) is equivalent to a CDS (Coding Sequence). === Populated Subsystem === please see [[#Subsystem|Subsystem]] === Subsystem === A subsystem is a set of functional roles that an annotator has decided should be thought of as related. Frequently, subsystems represent the collection of [[#Functional_role|functional roles]] that make up a metabolic pathway, a complex (e.g., the ribosome), or a class of proteins (e.g., two-component signal-transduction proteins within Staphylococcus aureus). A '''populated subsystem''' is a subsystem with an attached spreadsheet. The rows of the spreadsheet represent genomes and the columns represent the functional roles of the spreadsheet. Each cell contains the identifiers of genes from the corresponding genome the implement the specific functional role. That is, a populated subsystem specifies which genes implement instances of the subsystem in each of the genomes. The rows of a populated genome are assigned variant codes which describe which of a set of possible variants of the subsystem exist within each genome (special codes expressing a total absence of the subsystem or remaining uncertainty exist). Construction of a large set of curated populated subsystems is at the center of the NMPDR and SEED annotation efforts. === Subsystem Clearing House === Since annotators can work on any machine (including the public SEED) the way to propagate subsystems is via [http://anno-2.nmpdr.org/FIG/p2p/ch.cgi Subsystem Clearing House web page]. ===SEED etymology=== 0d1618417e8cc0fc481eaf386f0275798fa487bc 1454 1453 2006-08-13T16:37:27Z FolkerMeyer 2 wikitext text/x-wiki === Annotators SEED === The master copy for all data in the SEED environment. Users can not access this password protected site. === Annotation === please see [[#Assigning_a_gene_function_and_annotation| Assigning a gene function and annotation]] === Assigning a gene function and annotation === Annotators assign gene functions to genes, and we call this process annotation. In most contexts, people use the term annotation to refer to assignments of function to the genes within a single organism. We certainly use the term in this sense, but we also use it to describe the process of assigning functions to corresponding genes from numerous genomes. Our basic approach to annotation is to ask our annotators to annotate the genes included in a [[#subsystem|Subsystem]] (e.g., glycolysis) across all genomes. This process of annotation of the genes within a subsystem across a set of genomes, rather than annotation of genes within a single genome, allows our annotators to focus on a constrained set of functional roles and attempt to accurately identify exactly what variant, if any, of a subsystem exists in each of the genomes. We use the term annotation to refer to assigning functions to genes (either within a single organism or to a constrained set of gene/protein families across a set of organisms). This activity certainly is closely related to the construction of subsystems and protein families (which we call FIGfams), but we will describe those activities elsewhere. === Assignment === please see [[#Assigning_a_gene_function_and_annotation| Assigning a gene function and annotation]] === Clearinghouse === please see [[#SubsystemClearinghouse|Subsystem Clearinghouse]] === FIGfam === FIGfams are protein families generated by the Fellowship for Interpretation of Genomes (FIG). These families are based on the collection of subsystems, as well as correspondences between genes in closely related strains (we describe the construction of FIGfams in a separate SOP). The important properties of these families are as follows: # Two PEGs which both occur within a single FIGfam are believed to have the same function. # There is a decision procedure associated with the family which can be invoked to determine whether or not a gene can be “safely” assigned the function associated with the family. === Functional role === The concept of functional role is both basic and primitive in the sense that we will not pretend to offer a precise definition. It corresponds roughly to a single logical role that a gene or gene product may play in the operation of a cell. === Gene function === The function of a protein-encoding gene (PEG) is the functional role played by the product of the gene or an expression describing a set of roles played by the encoded protein. The operators used to construct expressions and the meanings associated with the operators are described in http://www.nmpdr.org/FIG/Html/SEED_functions.html Genes other than PEGs can also be assigned functions (e.g., SSU rRNA). However, in most cases the functions assigned to genes other than PEGs tend not to be problematic. This document will focus solely on annotation of PEGs. === Metabolic Reconstruction When we use the term metabolic reconstruction of a given genome we will simply mean the set of populated subsystems that contain the genome, the PEGs (and their assigned functions) that are connected to functional roles in these populated subsystems, and the specific variant code associated with the genome in each of the populated subsystems. === NMPDR pathogen genome ===: The NMPDR is responsible for five classes of genomes: # Campylobacter jejuni # Listeria monocytogenes # Staphylococcus aureus # Streptococcus pneumoniae and Streptococcus pyogenes # Pathogenic Vibrio === PEG === A Protein Encoding Gene (PEG) is equivalent to a CDS (Coding Sequence). === Populated Subsystem === please see [[#Subsystem|Subsystem]] === Subsystem === A subsystem is a set of functional roles that an annotator has decided should be thought of as related. Frequently, subsystems represent the collection of [[#Functional_role|functional roles]] that make up a metabolic pathway, a complex (e.g., the ribosome), or a class of proteins (e.g., two-component signal-transduction proteins within Staphylococcus aureus). A '''populated subsystem''' is a subsystem with an attached spreadsheet. The rows of the spreadsheet represent genomes and the columns represent the functional roles of the spreadsheet. Each cell contains the identifiers of genes from the corresponding genome the implement the specific functional role. That is, a populated subsystem specifies which genes implement instances of the subsystem in each of the genomes. The rows of a populated genome are assigned '''variant codes''' which describe which of a set of possible variants of the subsystem exist within each genome (special codes expressing a total absence of the subsystem or remaining uncertainty exist). Construction of a large set of curated populated subsystems is at the center of the NMPDR and SEED annotation efforts. === Subsystem Clearing House === Since annotators can work on any machine (including the public SEED) the way to propagate subsystems is via [http://anno-2.nmpdr.org/FIG/p2p/ch.cgi Subsystem Clearing House web page]. ===SEED etymology=== === Variant Code=== please see [[#Subsystem|Subsystem]] f990ae1dc0b7e9c6bdc882f85b8683d6f2107f29 1455 1454 2006-08-13T16:39:02Z FolkerMeyer 2 wikitext text/x-wiki === Annotators SEED === The master copy for all data in the SEED environment. Users can not access this password protected site. === Annotation === please see [[#Assigning_a_gene_function_and_annotation| Assigning a gene function and annotation]] === Assigning a gene function and annotation === Annotators assign gene functions to genes, and we call this process annotation. In most contexts, people use the term annotation to refer to assignments of function to the genes within a single organism. We certainly use the term in this sense, but we also use it to describe the process of assigning functions to corresponding genes from numerous genomes. Our basic approach to annotation is to ask our annotators to annotate the genes included in a [[#subsystem|Subsystem]] (e.g., glycolysis) across all genomes. This process of annotation of the genes within a subsystem across a set of genomes, rather than annotation of genes within a single genome, allows our annotators to focus on a constrained set of functional roles and attempt to accurately identify exactly what variant, if any, of a subsystem exists in each of the genomes. We use the term annotation to refer to assigning functions to genes (either within a single organism or to a constrained set of gene/protein families across a set of organisms). This activity certainly is closely related to the construction of subsystems and protein families (which we call FIGfams), but we will describe those activities elsewhere. === Assignment === please see [[#Assigning_a_gene_function_and_annotation| Assigning a gene function and annotation]] === Clearinghouse === please see [[#SubsystemClearinghouse|Subsystem Clearinghouse]] === FIGfam === FIGfams are protein families generated by the Fellowship for Interpretation of Genomes (FIG). These families are based on the collection of subsystems, as well as correspondences between genes in closely related strains (we describe the construction of FIGfams in a separate SOP). The important properties of these families are as follows: # Two PEGs which both occur within a single FIGfam are believed to have the same function. # There is a decision procedure associated with the family which can be invoked to determine whether or not a gene can be “safely” assigned the function associated with the family. === Functional role === The concept of functional role is both basic and primitive in the sense that we will not pretend to offer a precise definition. It corresponds roughly to a single logical role that a gene or gene product may play in the operation of a cell. === Gene function === The function of a protein-encoding gene (PEG) is the functional role played by the product of the gene or an expression describing a set of roles played by the encoded protein. The operators used to construct expressions and the meanings associated with the operators are described in http://www.nmpdr.org/FIG/Html/SEED_functions.html Genes other than PEGs can also be assigned functions (e.g., SSU rRNA). However, in most cases the functions assigned to genes other than PEGs tend not to be problematic. This document will focus solely on annotation of PEGs. === Metabolic Reconstruction === When we use the term metabolic reconstruction of a given genome we will simply mean the set of populated subsystems that contain the genome, the PEGs (and their assigned functions) that are connected to functional roles in these populated subsystems, and the specific variant code associated with the genome in each of the populated subsystems. === NMPDR pathogen genome === The NMPDR is responsible for five classes of genomes: # Campylobacter jejuni # Listeria monocytogenes # Staphylococcus aureus # Streptococcus pneumoniae and Streptococcus pyogenes # Pathogenic Vibrio === PEG === A Protein Encoding Gene (PEG) is equivalent to a CDS (Coding Sequence). === Populated Subsystem === please see [[#Subsystem|Subsystem]] === Subsystem === A subsystem is a set of functional roles that an annotator has decided should be thought of as related. Frequently, subsystems represent the collection of [[#Functional_role|functional roles]] that make up a metabolic pathway, a complex (e.g., the ribosome), or a class of proteins (e.g., two-component signal-transduction proteins within Staphylococcus aureus). A '''populated subsystem''' is a subsystem with an attached spreadsheet. The rows of the spreadsheet represent genomes and the columns represent the functional roles of the spreadsheet. Each cell contains the identifiers of genes from the corresponding genome the implement the specific functional role. That is, a populated subsystem specifies which genes implement instances of the subsystem in each of the genomes. The rows of a populated genome are assigned '''variant codes''' which describe which of a set of possible variants of the subsystem exist within each genome (special codes expressing a total absence of the subsystem or remaining uncertainty exist). Construction of a large set of curated populated subsystems is at the center of the NMPDR and SEED annotation efforts. === Subsystem Clearing House === Since annotators can work on any machine (including the public SEED) the way to propagate subsystems is via [http://clearinghouse.theseed.org/clearinghouse_browser.cgi? Subsystem Clearing House web page]. ===SEED etymology=== === Variant Code=== please see [[#Subsystem|Subsystem]] dc5d4509db0a8f6adf1f5e3a8d2ed2eaae5f319e 1456 1455 2006-08-13T16:41:55Z FolkerMeyer 2 wikitext text/x-wiki === Annotators SEED === The master copy for all data in the SEED environment. Users can not access this password protected site. All annotations are made available via the [http://explorer.theseed.org/FIG/index.cgi SEED-Viewer] (update every 24 hours) and the [http://theseed.uchicago.edu/FIG/index.cgi Trial-SEED] (updated in irregular intervals). === Annotation === please see [[#Assigning_a_gene_function_and_annotation| Assigning a gene function and annotation]] === Assigning a gene function and annotation === Annotators assign gene functions to genes, and we call this process annotation. In most contexts, people use the term annotation to refer to assignments of function to the genes within a single organism. We certainly use the term in this sense, but we also use it to describe the process of assigning functions to corresponding genes from numerous genomes. Our basic approach to annotation is to ask our annotators to annotate the genes included in a [[#subsystem|Subsystem]] (e.g., glycolysis) across all genomes. This process of annotation of the genes within a subsystem across a set of genomes, rather than annotation of genes within a single genome, allows our annotators to focus on a constrained set of functional roles and attempt to accurately identify exactly what variant, if any, of a subsystem exists in each of the genomes. We use the term annotation to refer to assigning functions to genes (either within a single organism or to a constrained set of gene/protein families across a set of organisms). This activity certainly is closely related to the construction of subsystems and protein families (which we call FIGfams), but we will describe those activities elsewhere. === Assignment === please see [[#Assigning_a_gene_function_and_annotation| Assigning a gene function and annotation]] === Clearinghouse === please see [[#SubsystemClearinghouse|Subsystem Clearinghouse]] === FIGfam === FIGfams are protein families generated by the Fellowship for Interpretation of Genomes (FIG). These families are based on the collection of subsystems, as well as correspondences between genes in closely related strains (we describe the construction of FIGfams in a separate SOP). The important properties of these families are as follows: # Two PEGs which both occur within a single FIGfam are believed to have the same function. # There is a decision procedure associated with the family which can be invoked to determine whether or not a gene can be “safely” assigned the function associated with the family. === Functional role === The concept of functional role is both basic and primitive in the sense that we will not pretend to offer a precise definition. It corresponds roughly to a single logical role that a gene or gene product may play in the operation of a cell. === Gene function === The function of a protein-encoding gene (PEG) is the functional role played by the product of the gene or an expression describing a set of roles played by the encoded protein. The operators used to construct expressions and the meanings associated with the operators are described in http://www.nmpdr.org/FIG/Html/SEED_functions.html Genes other than PEGs can also be assigned functions (e.g., SSU rRNA). However, in most cases the functions assigned to genes other than PEGs tend not to be problematic. This document will focus solely on annotation of PEGs. === Metabolic Reconstruction === When we use the term metabolic reconstruction of a given genome we will simply mean the set of populated subsystems that contain the genome, the PEGs (and their assigned functions) that are connected to functional roles in these populated subsystems, and the specific variant code associated with the genome in each of the populated subsystems. === NMPDR pathogen genome === The NMPDR is responsible for five classes of genomes: # Campylobacter jejuni # Listeria monocytogenes # Staphylococcus aureus # Streptococcus pneumoniae and Streptococcus pyogenes # Pathogenic Vibrio === PEG === A Protein Encoding Gene (PEG) is equivalent to a CDS (Coding Sequence). === Populated Subsystem === please see [[#Subsystem|Subsystem]] === Subsystem === A subsystem is a set of functional roles that an annotator has decided should be thought of as related. Frequently, subsystems represent the collection of [[#Functional_role|functional roles]] that make up a metabolic pathway, a complex (e.g., the ribosome), or a class of proteins (e.g., two-component signal-transduction proteins within Staphylococcus aureus). A '''populated subsystem''' is a subsystem with an attached spreadsheet. The rows of the spreadsheet represent genomes and the columns represent the functional roles of the spreadsheet. Each cell contains the identifiers of genes from the corresponding genome the implement the specific functional role. That is, a populated subsystem specifies which genes implement instances of the subsystem in each of the genomes. The rows of a populated genome are assigned '''variant codes''' which describe which of a set of possible variants of the subsystem exist within each genome (special codes expressing a total absence of the subsystem or remaining uncertainty exist). Construction of a large set of curated populated subsystems is at the center of the NMPDR and SEED annotation efforts. === Subsystem Clearing House === Since annotators can work on any machine (including the public SEED) the way to propagate subsystems is via [http://clearinghouse.theseed.org/clearinghouse_browser.cgi? Subsystem Clearing House web page]. ===SEED etymology=== === Variant Code=== please see [[#Subsystem|Subsystem]] deff6542e2f4f03f11ff51d5c1098394717f898c 1457 1456 2006-08-13T16:48:17Z FolkerMeyer 2 wikitext text/x-wiki === Annotators SEED === The master copy for all data in the SEED environment. Users can not access this password protected site. All annotations are made available via the [[#SEED-Viewer| SEED-Viewer]] and the [[#Trial-SEED|Trial-SEED]]. === Annotation === please see [[#Assigning_a_gene_function_and_annotation| Assigning a gene function and annotation]] === Assigning a gene function and annotation === Annotators assign gene functions to genes, and we call this process annotation. In most contexts, people use the term annotation to refer to assignments of function to the genes within a single organism. We certainly use the term in this sense, but we also use it to describe the process of assigning functions to corresponding genes from numerous genomes. Our basic approach to annotation is to ask our annotators to annotate the genes included in a [[#subsystem|Subsystem]] (e.g., glycolysis) across all genomes. This process of annotation of the genes within a subsystem across a set of genomes, rather than annotation of genes within a single genome, allows our annotators to focus on a constrained set of functional roles and attempt to accurately identify exactly what variant, if any, of a subsystem exists in each of the genomes. We use the term annotation to refer to assigning functions to genes (either within a single organism or to a constrained set of gene/protein families across a set of organisms). This activity certainly is closely related to the construction of subsystems and protein families (which we call FIGfams), but we will describe those activities elsewhere. === Assignment === please see [[#Assigning_a_gene_function_and_annotation| Assigning a gene function and annotation]] === Clearinghouse === please see [[#SubsystemClearinghouse|Subsystem Clearinghouse]] === FIGfam === FIGfams are protein families generated by the Fellowship for Interpretation of Genomes (FIG). These families are based on the collection of subsystems, as well as correspondences between genes in closely related strains (we describe the construction of FIGfams in a separate SOP). The important properties of these families are as follows: # Two PEGs which both occur within a single FIGfam are believed to have the same function. # There is a decision procedure associated with the family which can be invoked to determine whether or not a gene can be “safely” assigned the function associated with the family. === Functional role === The concept of functional role is both basic and primitive in the sense that we will not pretend to offer a precise definition. It corresponds roughly to a single logical role that a gene or gene product may play in the operation of a cell. === Gene function === The function of a protein-encoding gene (PEG) is the functional role played by the product of the gene or an expression describing a set of roles played by the encoded protein. The operators used to construct expressions and the meanings associated with the operators are described in http://www.nmpdr.org/FIG/Html/SEED_functions.html Genes other than PEGs can also be assigned functions (e.g., SSU rRNA). However, in most cases the functions assigned to genes other than PEGs tend not to be problematic. This document will focus solely on annotation of PEGs. === Metabolic Reconstruction === When we use the term metabolic reconstruction of a given genome we will simply mean the set of populated subsystems that contain the genome, the PEGs (and their assigned functions) that are connected to functional roles in these populated subsystems, and the specific variant code associated with the genome in each of the populated subsystems. === NMPDR pathogen genome === The NMPDR is responsible for five classes of genomes: # Campylobacter jejuni # Listeria monocytogenes # Staphylococcus aureus # Streptococcus pneumoniae and Streptococcus pyogenes # Pathogenic Vibrio === PEG === A Protein Encoding Gene (PEG) is equivalent to a CDS (Coding Sequence). === Populated Subsystem === please see [[#Subsystem|Subsystem]] === SEED-Viewer === A read-only version of the SEED that presents the latest data. http://seed-viewer.theseed.org '''Please note''': The data is updated automatically every 24 hours. When citing or linking to the SEED please use this version. === Subsystem === A subsystem is a set of functional roles that an annotator has decided should be thought of as related. Frequently, subsystems represent the collection of [[#Functional_role|functional roles]] that make up a metabolic pathway, a complex (e.g., the ribosome), or a class of proteins (e.g., two-component signal-transduction proteins within Staphylococcus aureus). A '''populated subsystem''' is a subsystem with an attached spreadsheet. The rows of the spreadsheet represent genomes and the columns represent the functional roles of the spreadsheet. Each cell contains the identifiers of genes from the corresponding genome the implement the specific functional role. That is, a populated subsystem specifies which genes implement instances of the subsystem in each of the genomes. The rows of a populated genome are assigned '''variant codes''' which describe which of a set of possible variants of the subsystem exist within each genome (special codes expressing a total absence of the subsystem or remaining uncertainty exist). Construction of a large set of curated populated subsystems is at the center of the NMPDR and SEED annotation efforts. === Subsystem Clearing House === Since annotators can work on any machine (including the public SEED) the way to propagate subsystems is via [http://clearinghouse.theseed.org/clearinghouse_browser.cgi? Subsystem Clearing House web page]. ===SEED etymology=== === Trial-SEED === A public, read-write copy of the SEED is made available on http://theseed.uchicago.edu/FIG/index.cgi '''Please note''': The data on this server is updated in irregular intervals. Users should not assume that annotations made on this system will persist. Please publish your annotations to the [[#Subsystem_clearing_house|Subsystem Clearing house]]. === Variant Code=== please see [[#Subsystem|Subsystem]] 519c4b1a9b017b8fdeb04199f57e8b3880a4f90f 1458 1457 2006-08-13T16:49:38Z FolkerMeyer 2 wikitext text/x-wiki === Annotators SEED === The master copy for all data in the SEED environment. Users can not access this password protected site. All annotations are made available via the [[#SEED-Viewer| SEED-Viewer]] and the [[#Trial-SEED|Trial-SEED]]. === Annotation === please see [[#Assigning_a_gene_function_and_annotation| Assigning a gene function and annotation]] === Assigning a gene function and annotation === Annotators assign gene functions to genes, and we call this process annotation. In most contexts, people use the term annotation to refer to assignments of function to the genes within a single organism. We certainly use the term in this sense, but we also use it to describe the process of assigning functions to corresponding genes from numerous genomes. Our basic approach to annotation is to ask our annotators to annotate the genes included in a [[#subsystem|Subsystem]] (e.g., glycolysis) across all genomes. This process of annotation of the genes within a subsystem across a set of genomes, rather than annotation of genes within a single genome, allows our annotators to focus on a constrained set of functional roles and attempt to accurately identify exactly what variant, if any, of a subsystem exists in each of the genomes. We use the term annotation to refer to assigning functions to genes (either within a single organism or to a constrained set of gene/protein families across a set of organisms). This activity certainly is closely related to the construction of subsystems and protein families (which we call FIGfams), but we will describe those activities elsewhere. === Assignment === please see [[#Assigning_a_gene_function_and_annotation| Assigning a gene function and annotation]] === Clearinghouse === please see [[#SubsystemClearinghouse|Subsystem Clearinghouse]] === FIGfam === FIGfams are protein families generated by the Fellowship for Interpretation of Genomes (FIG). These families are based on the collection of subsystems, as well as correspondences between genes in closely related strains (we describe the construction of FIGfams in a separate SOP). The important properties of these families are as follows: # Two PEGs which both occur within a single FIGfam are believed to have the same function. # There is a decision procedure associated with the family which can be invoked to determine whether or not a gene can be “safely” assigned the function associated with the family. === Functional role === The concept of functional role is both basic and primitive in the sense that we will not pretend to offer a precise definition. It corresponds roughly to a single logical role that a gene or gene product may play in the operation of a cell. === Gene function === The function of a protein-encoding gene (PEG) is the functional role played by the product of the gene or an expression describing a set of roles played by the encoded protein. The operators used to construct expressions and the meanings associated with the operators are described in http://www.nmpdr.org/FIG/Html/SEED_functions.html Genes other than PEGs can also be assigned functions (e.g., SSU rRNA). However, in most cases the functions assigned to genes other than PEGs tend not to be problematic. This document will focus solely on annotation of PEGs. === Metabolic Reconstruction === When we use the term metabolic reconstruction of a given genome we will simply mean the set of populated subsystems that contain the genome, the PEGs (and their assigned functions) that are connected to functional roles in these populated subsystems, and the specific variant code associated with the genome in each of the populated subsystems. === NMPDR pathogen genome === The NMPDR is responsible for five classes of genomes: # Campylobacter jejuni # Listeria monocytogenes # Staphylococcus aureus # Streptococcus pneumoniae and Streptococcus pyogenes # Pathogenic Vibrio === PEG === A Protein Encoding Gene (PEG) is equivalent to a CDS (Coding Sequence). === Populated Subsystem === please see [[#Subsystem|Subsystem]] === SEED-Viewer === A read-only version of the SEED that presents the latest data. http://seed-viewer.theseed.org '''Please note''': The data is updated automatically every 24 hours. When citing or linking to the SEED please use this version. === Subsystem === A subsystem is a set of functional roles that an annotator has decided should be thought of as related. Frequently, subsystems represent the collection of [[#Functional_role|functional roles]] that make up a metabolic pathway, a complex (e.g., the ribosome), or a class of proteins (e.g., two-component signal-transduction proteins within Staphylococcus aureus). A '''populated subsystem''' is a subsystem with an attached spreadsheet. The rows of the spreadsheet represent genomes and the columns represent the functional roles of the spreadsheet. Each cell contains the identifiers of genes from the corresponding genome the implement the specific functional role. That is, a populated subsystem specifies which genes implement instances of the subsystem in each of the genomes. The rows of a populated genome are assigned '''variant codes''' which describe which of a set of possible variants of the subsystem exist within each genome (special codes expressing a total absence of the subsystem or remaining uncertainty exist). Construction of a large set of curated populated subsystems is at the center of the NMPDR and SEED annotation efforts. === Subsystem Clearing House === Since annotators can work on any machine (including the public SEED) the way to propagate subsystems is via http://clearinghouse.theseed.org/clearinghouse_browser.cgi? ===SEED etymology=== === Trial-SEED === A public, read-write copy of the SEED is made available on http://theseed.uchicago.edu/FIG/index.cgi '''Please note''': The data on this server is updated in irregular intervals. Users should not assume that annotations made on this system will persist. Please publish your annotations to the [[#Subsystem_clearing_house|Subsystem Clearing house]]. === Variant Code=== please see [[#Subsystem|Subsystem]] 7511fc84eaeb199709dd816fb789fde508655e47 1459 1458 2006-08-13T16:50:08Z FolkerMeyer 2 wikitext text/x-wiki === Annotators SEED === The master copy for all data in the SEED environment. Users can not access this password protected site. All annotations are made available via the [[#SEED-Viewer| SEED-Viewer]] and the [[#Trial-SEED|Trial-SEED]]. === Annotation === please see [[#Assigning_a_gene_function_and_annotation| Assigning a gene function and annotation]] === Assigning a gene function and annotation === Annotators assign gene functions to genes, and we call this process annotation. In most contexts, people use the term annotation to refer to assignments of function to the genes within a single organism. We certainly use the term in this sense, but we also use it to describe the process of assigning functions to corresponding genes from numerous genomes. Our basic approach to annotation is to ask our annotators to annotate the genes included in a [[#subsystem|Subsystem]] (e.g., glycolysis) across all genomes. This process of annotation of the genes within a subsystem across a set of genomes, rather than annotation of genes within a single genome, allows our annotators to focus on a constrained set of functional roles and attempt to accurately identify exactly what variant, if any, of a subsystem exists in each of the genomes. We use the term annotation to refer to assigning functions to genes (either within a single organism or to a constrained set of gene/protein families across a set of organisms). This activity certainly is closely related to the construction of subsystems and protein families (which we call FIGfams), but we will describe those activities elsewhere. === Assignment === please see [[#Assigning_a_gene_function_and_annotation| Assigning a gene function and annotation]] === Clearinghouse === please see [[#SubsystemClearinghouse|Subsystem Clearinghouse]] === FIGfam === FIGfams are protein families generated by the Fellowship for Interpretation of Genomes (FIG). These families are based on the collection of subsystems, as well as correspondences between genes in closely related strains (we describe the construction of FIGfams in a separate SOP). The important properties of these families are as follows: # Two PEGs which both occur within a single FIGfam are believed to have the same function. # There is a decision procedure associated with the family which can be invoked to determine whether or not a gene can be “safely” assigned the function associated with the family. === Functional role === The concept of functional role is both basic and primitive in the sense that we will not pretend to offer a precise definition. It corresponds roughly to a single logical role that a gene or gene product may play in the operation of a cell. === Gene function === The function of a protein-encoding gene (PEG) is the functional role played by the product of the gene or an expression describing a set of roles played by the encoded protein. The operators used to construct expressions and the meanings associated with the operators are described in http://www.nmpdr.org/FIG/Html/SEED_functions.html Genes other than PEGs can also be assigned functions (e.g., SSU rRNA). However, in most cases the functions assigned to genes other than PEGs tend not to be problematic. This document will focus solely on annotation of PEGs. === Metabolic Reconstruction === When we use the term metabolic reconstruction of a given genome we will simply mean the set of populated subsystems that contain the genome, the PEGs (and their assigned functions) that are connected to functional roles in these populated subsystems, and the specific variant code associated with the genome in each of the populated subsystems. === NMPDR pathogen genome === The NMPDR is responsible for five classes of genomes: # Campylobacter jejuni # Listeria monocytogenes # Staphylococcus aureus # Streptococcus pneumoniae and Streptococcus pyogenes # Pathogenic Vibrio === PEG === A Protein Encoding Gene (PEG) is equivalent to a CDS (Coding Sequence). === Populated Subsystem === please see [[#Subsystem|Subsystem]] === SEED-Viewer === A read-only version of the SEED that presents the latest data. http://seed-viewer.theseed.org '''Please note''': The data is updated automatically every 24 hours. When citing or linking to the SEED please use this version. === Subsystem === A subsystem is a set of functional roles that an annotator has decided should be thought of as related. Frequently, subsystems represent the collection of [[#Functional_role|functional roles]] that make up a metabolic pathway, a complex (e.g., the ribosome), or a class of proteins (e.g., two-component signal-transduction proteins within Staphylococcus aureus). A '''populated subsystem''' is a subsystem with an attached spreadsheet. The rows of the spreadsheet represent genomes and the columns represent the functional roles of the spreadsheet. Each cell contains the identifiers of genes from the corresponding genome the implement the specific functional role. That is, a populated subsystem specifies which genes implement instances of the subsystem in each of the genomes. The rows of a populated genome are assigned '''variant codes''' which describe which of a set of possible variants of the subsystem exist within each genome (special codes expressing a total absence of the subsystem or remaining uncertainty exist). Construction of a large set of curated populated subsystems is at the center of the NMPDR and SEED annotation efforts. === Subsystem Clearing House === Since annotators can work on any machine (including the public SEED) the way to propagate subsystems is via http://clearinghouse.theseed.org/clearinghouse_browser.cgi? === Trial-SEED === A public, read-write copy of the SEED is made available on http://theseed.uchicago.edu/FIG/index.cgi '''Please note''': The data on this server is updated in irregular intervals. Users should not assume that annotations made on this system will persist. Please publish your annotations to the [[#Subsystem_clearing_house|Subsystem Clearing house]]. === Variant Code=== please see [[#Subsystem|Subsystem]] 2c08c6feb8974fd3ca843a89349b2ec1ec930e8d 1460 1459 2006-08-13T16:51:11Z FolkerMeyer 2 wikitext text/x-wiki === Annotators SEED === The master copy for all data in the SEED environment. Users can not access this password protected site. All annotations are made available via the [[#SEED-Viewer| SEED-Viewer]] and the [[#Trial-SEED|Trial-SEED]]. === Annotation === please see [[#Assigning_a_gene_function_and_annotation| Assigning a gene function and annotation]] === Assigning a gene function and annotation === Annotators assign gene functions to genes, and we call this process annotation. In most contexts, people use the term annotation to refer to assignments of function to the genes within a single organism. We certainly use the term in this sense, but we also use it to describe the process of assigning functions to corresponding genes from numerous genomes. Our basic approach to annotation is to ask our annotators to annotate the genes included in a [[#subsystem|Subsystem]] (e.g., glycolysis) across all genomes. This process of annotation of the genes within a subsystem across a set of genomes, rather than annotation of genes within a single genome, allows our annotators to focus on a constrained set of functional roles and attempt to accurately identify exactly what variant, if any, of a subsystem exists in each of the genomes. We use the term annotation to refer to assigning functions to genes (either within a single organism or to a constrained set of gene/protein families across a set of organisms). This activity certainly is closely related to the construction of subsystems and protein families (which we call FIGfams), but we will describe those activities elsewhere. === Assignment === please see [[#Assigning_a_gene_function_and_annotation| Assigning a gene function and annotation]] === Clearinghouse === please see [[#SubsystemClearinghouse|Subsystem Clearinghouse]] === FIGfam === FIGfams are protein families generated by the Fellowship for Interpretation of Genomes (FIG). These families are based on the collection of subsystems, as well as correspondences between genes in closely related strains (we describe the construction of FIGfams in a separate SOP). The important properties of these families are as follows: # Two PEGs which both occur within a single FIGfam are believed to have the same function. # There is a decision procedure associated with the family which can be invoked to determine whether or not a gene can be “safely” assigned the function associated with the family. === Functional role === The concept of functional role is both basic and primitive in the sense that we will not pretend to offer a precise definition. It corresponds roughly to a single logical role that a gene or gene product may play in the operation of a cell. === Gene function === The function of a protein-encoding gene (PEG) is the functional role played by the product of the gene or an expression describing a set of roles played by the encoded protein. The operators used to construct expressions and the meanings associated with the operators are described in http://www.nmpdr.org/FIG/Html/SEED_functions.html Genes other than PEGs can also be assigned functions (e.g., SSU rRNA). However, in most cases the functions assigned to genes other than PEGs tend not to be problematic. === Metabolic Reconstruction === When we use the term metabolic reconstruction of a given genome we will simply mean the set of populated subsystems that contain the genome, the PEGs (and their assigned functions) that are connected to functional roles in these populated subsystems, and the specific variant code associated with the genome in each of the populated subsystems. === NMPDR pathogen genome === The NMPDR is responsible for five classes of genomes: # Campylobacter jejuni # Listeria monocytogenes # Staphylococcus aureus # Streptococcus pneumoniae and Streptococcus pyogenes # Pathogenic Vibrio === PEG === A Protein Encoding Gene (PEG) is equivalent to a CDS (Coding Sequence). === Populated Subsystem === please see [[#Subsystem|Subsystem]] === SEED-Viewer === A read-only version of the SEED that presents the latest data. http://seed-viewer.theseed.org '''Please note''': The data is updated automatically every 24 hours. When citing or linking to the SEED please use this version. === Subsystem === A subsystem is a set of functional roles that an annotator has decided should be thought of as related. Frequently, subsystems represent the collection of [[#Functional_role|functional roles]] that make up a metabolic pathway, a complex (e.g., the ribosome), or a class of proteins (e.g., two-component signal-transduction proteins within Staphylococcus aureus). A '''populated subsystem''' is a subsystem with an attached spreadsheet. The rows of the spreadsheet represent genomes and the columns represent the functional roles of the spreadsheet. Each cell contains the identifiers of genes from the corresponding genome the implement the specific functional role. That is, a populated subsystem specifies which genes implement instances of the subsystem in each of the genomes. The rows of a populated genome are assigned '''variant codes''' which describe which of a set of possible variants of the subsystem exist within each genome (special codes expressing a total absence of the subsystem or remaining uncertainty exist). Construction of a large set of curated populated subsystems is at the center of the NMPDR and SEED annotation efforts. === Subsystem Clearing House === Since annotators can work on any machine (including the public SEED) the way to propagate subsystems is via http://clearinghouse.theseed.org/clearinghouse_browser.cgi? === Trial-SEED === A public, read-write copy of the SEED is made available on http://theseed.uchicago.edu/FIG/index.cgi '''Please note''': The data on this server is updated in irregular intervals. Users should not assume that annotations made on this system will persist. Please publish your annotations to the [[#Subsystem_clearing_house|Subsystem Clearing house]]. === Variant Code=== please see [[#Subsystem|Subsystem]] bd23f2aec259da9e2227b0699fd1c621c5c4faa3 0 1380 1464 2006-08-13T23:08:42Z VeronikaVonstein 6 [[Annotation]] moved to [[Annotation of close strains]] wikitext text/x-wiki #REDIRECT [[Annotation of close strains]] 4b5cd4250a0261264f9ff47983e64e82020a7f9d 0 1379 1465 1463 2006-08-13T23:12:22Z FolkerMeyer 2 [[Annotation of close strains]] moved to [[Annotation of close strain sets]] wikitext text/x-wiki == Annotation of Genomes: == === Standard Operating Procedure === === Introduction === This procedure describes the annotation process used by the SEED and NMPDR annotators and curators. Let us begin by discussing a number of terms that we use in this document: '''Functional Role''': The concept of functional role is both basic and primitive in the sense that we will not pretend to offer a precise definition. It corresponds roughly to a single logical role that a gene or gene product may play in the operation of a cell. '''Gene function''': The function of a protein-encoding gene (PEG) is the functional role played by the product of the gene or an expression describing a set of roles played by the encoded protein. The operators used to construct expressions and the meanings associated with the operators are described in http://www.nmpdr.org/FIG/Html/SEED_functions.html Genes other than PEGs can also be assigned functions (e.g., SSU rRNA). However, in most cases the functions assigned to genes other than PEGs tend not to be problematic. This document will focus solely on annotation of PEGs. '''Assigning a gene function and annotation''': Annotators assign gene functions to genes, and we call this process annotation. In most contexts, people use the term annotation to refer to assignments of function to the genes within a single organism. We certainly use the term in this sense, but we also use it to describe the process of assigning functions to corresponding genes from numerous genomes. Our basic approach to annotation is to ask our annotators to annotate the genes included in a subsystem (e.g., glycolysis) across all genomes. This process of annotation of the genes within a subsystem across a set of genomes, rather than annotation of genes within a single genome, allows our annotators to focus on a constrained set of functional roles and attempt to accurately identify exactly what variant, if any, of a subsystem exists in each of the genomes. We use the term annotation to refer to assigning functions to genes (either within a single organism or to a constrained set of gene/protein families across a set of organisms). This activity certainly is closely related to the construction of subsystems and protein families (which we call FIGfams), but we will describe those activities elsewhere. '''Subsystem''': A subsystem is a set of functional roles that an annotator has decided should be thought of as related. Frequently, subsystems represent the collection of functional roles that make up a metabolic pathway, a complex (e.g., the ribosome), or a class of proteins (e.g., two-component signal-transduction proteins within Staphylococcus aureus). A populated subsystem is a subsystem with an attached spreadsheet. The rows of the spreadsheet represent genomes and the columns represent the functional roles of the spreadsheet. Each cell contains the identifiers of genes from the corresponding genome the implement the specific functional role. That is, a populated subsystem specifies which genes implement instances of the subsystem in each of the genomes. The rows of a populated genome are assigned variant codes which describe which of a set of possible variants of the subsystem exist within each genome (special codes expressing a total absence of the subsystem or remaining uncertainty exist). Construction of a large set of curated populated subsystems is at the center of the NMPDR and SEED annotation efforts. '''FIGfam''': FIGfams are protein families generated by the Fellowship for Interpretation of Genomes (FIG). These families are based on the collection of subsystems, as well as correspondences between genes in closely related strains (we describe the construction of FIGfams in a separate SOP). The important properties of these families are as follows: # Two PEGs which both occur within a single FIGfam are believed to have the same function. # There is a decision procedure associated with the family which can be invoked to determine whether or not a gene can be “safely” assigned the function associated with the family. '''Metabolic Reconstruction''': When we use the term metabolic reconstruction of a given genome we will simply mean the set of populated subsystems that contain the genome, the PEGs (and their assigned functions) that are connected to functional roles in these populated subsystems, and the specific variant code associated with the genome in each of the populated subsystems. '''NMPDR pathogen genome''': The NMPDR is responsible for five classes of genomes: # Campylobacter jejuni # Listeria monocytogenes # Staphylococcus aureus # Streptococcus pneumoniae and Streptococcus pyogenes # Pathogenic Vibrio We refer to these genomes as the NMPDR pathogens. The NMPDR carefully annotates some close relatives of these classes to provide accurate comparative context. Similarly, it includes a diverse collection of complete genomes that it annotates less accurately to provide context for comparative analysis. Now we can discuss what we mean by the annotations and the standard procedure for making those annotations. === The Annotation Procedure === The annotation of genomes begins after the genes have been identified and the genome has been integrated into a SEED environment. The annotation process then proceeds through the following steps: # Use of FIGfams # Use of Subsystems # Annotation of Prophages # Resolution of Conflicts # Improvement of Annotation Via New Subsystems # Continuous Refinement Via Analysis of Literature The following sections cover each of these steps in detail. We present the sequence of steps as commands issued from the command line. In fact, we are constructing a pipeline managed from a web interface that is intended to allow a relatively unskilled user to control the process. ==== Step 1: Use of FIGfams ==== For each new genome, we form a set of anticipated families by gathering all FIGfams with members in genomes from the same class. We begin the annotation by taking the anticipated families and searching for occurrences of these FIGfams within the new genome. This is achieved by invoking install_anticipated_functions User GenomeToBeAnnotated FileOfGenomesGivingContext Where User is the individual issuing the command, GenomeToBeAnnotated is the ID of the genome to be annotated (it is assumed that this genome has already been installed in the current SEED), and FileOfGenomesGivingContext is a file containing genome IDs (one per line) of the existing genomes from the same class. The effect of running this command will be to locate the instances of families when possible, to assign the appropriate function to the located genes, and to record detailed annotations of which FIGfam families were used as the basis for each annotation (along with the User and timestamps). ==== Step 2: Use of Subsystems ==== Once initial assignments based on FIGfams has been accomplished, it is possible to rapidly assess the presence and absence of subsystems (it is worth noting that every functional role within existing subsystems is covered by a FIGfam). The process begins with potentially_missed_assignments GenomeToBeAnnotated FileOfGenomesGivingContext This command will produce a list of assignments that may have been missed. This list is formed by looking at subsystems contained in each of the genomes that make up the context, checking for subsystems in which a majority (but not all) of the genes have corresponding genes in the new genome, and candidates for the missing genes can be located. The tool produces a list of possibly missed assignments that must be checked by an annotator. Once the list of possibly missed assignments has been processed, the following command can be run: add_to_subsystems User GenomeToBeAnnotated FileOfGenomesGivingContext This command will compute the set of subsystems from the context genomes for which all of the corresponding genes can be located in the new genome. This set of subsystems will then be split into two lists: # Some of the subsystems are marked as automatically extendable by their curators. For these subsystems, the new genome will be added to the populated subsystem. # For those subsystems that are not marked as automatically extendable, the fact that the new genome should be added to the subsystem will be recorded. Curators for these subsystems will be notified and asked to add the new genome. The tentative metabolic reconstruction is formed (including subsystems from both lists). ==== Step 3: Annotation of Prophages and Mobil Elements ==== For each class of NMPDR pathogen we maintain as features a list of prophages and other mobil elements. Execution of mark_features prophage User GenomeToBeAnnotated FileOfGenomesGivingContext mark_features mobil_element User GenomeToBeAnnotated FileOfGenomesGivingContext will cause instances of these prohages and other mobile elements to be detected and marked as features in the new genome. These annotations will be logged. ==== Step 4: Resolution of Conflicts ==== FIGfams are not always annotated consistently. This can happen in cases in which it is possible to assert that a set of genes have a common function, but for which disagreement remains about exactly how to label the role played by members of the family. In such cases, a functional role is associated with the FIGfam, but individual members of the family may have distinct (inconsistent) functions. The number of such instances is gradually dropping, but we have adopted the position that it is better to retain the inconsistency (reflecting real uncertainty) rather than enforcing a common function. Execution of the following command will produce a list of conflicts that should be examined by an annotator: potential_conflicts GenomeToBeAnnotated FileOfGenomesGivingContext ==== Step 5: Improvement of Annotation Via New Subsystems ==== Normal subsystem maintenance occurs constantly. The basic activity of our annotators is to extend existing subsystems and to define and populate new subsystems. These activities produce a gradual improvement in the quality of annotations for all genomes. All new annotations are logged as they are made. ==== Step 6: Continuous Refinement Via Analysis of Literature ==== Annotators should continuously review new literature, seeking cases in which gene functions can be improved based on new results. Sometimes, this results in improvements in function for a specific gene (and these results are then propagated to other members of the NMPDR pathogen class). More often, these new results are used as the basis for new subsystems and have a broader impact. c3f99926f85ab981bdd3998caa567334004051e7 1472 1465 2006-08-16T16:08:12Z FolkerMeyer 2 wikitext text/x-wiki == Annotation of Genomes: == === Standard Operating Procedure === === Introduction === This procedure describes the annotation process used by the SEED and NMPDR annotators and curators. Let us begin by discussing a number of terms that we use in this document: '''Functional Role''': The concept of functional role is both basic and primitive in the sense that we will not pretend to offer a precise definition. It corresponds roughly to a single logical role that a gene or gene product may play in the operation of a cell. '''Gene function''': The function of a protein-encoding gene (PEG) is the functional role played by the product of the gene or an expression describing a set of roles played by the encoded protein. The operators used to construct expressions and the meanings associated with the operators are described in http://www.nmpdr.org/FIG/Html/SEED_functions.html Genes other than PEGs can also be assigned functions (e.g., SSU rRNA). However, in most cases the functions assigned to genes other than PEGs tend not to be problematic. This document will focus solely on annotation of PEGs. '''Assigning a gene function and annotation''': Annotators assign gene functions to genes, and we call this process annotation. In most contexts, people use the term annotation to refer to assignments of function to the genes within a single organism. We certainly use the term in this sense, but we also use it to describe the process of assigning functions to corresponding genes from numerous genomes. Our basic approach to annotation is to ask our annotators to annotate the genes included in a subsystem (e.g., glycolysis) across all genomes. This process of annotation of the genes within a subsystem across a set of genomes, rather than annotation of genes within a single genome, allows our annotators to focus on a constrained set of functional roles and attempt to accurately identify exactly what variant, if any, of a subsystem exists in each of the genomes. We use the term annotation to refer to assigning functions to genes (either within a single organism or to a constrained set of gene/protein families across a set of organisms). This activity certainly is closely related to the construction of subsystems and protein families (which we call FIGfams), but we will describe those activities elsewhere. '''Subsystem''': A subsystem is a set of functional roles that an annotator has decided should be thought of as related. Frequently, subsystems represent the collection of functional roles that make up a metabolic pathway, a complex (e.g., the ribosome), or a class of proteins (e.g., two-component signal-transduction proteins within Staphylococcus aureus). A populated subsystem is a subsystem with an attached spreadsheet. The rows of the spreadsheet represent genomes and the columns represent the functional roles of the spreadsheet. Each cell contains the identifiers of genes from the corresponding genome the implement the specific functional role. That is, a populated subsystem specifies which genes implement instances of the subsystem in each of the genomes. The rows of a populated genome are assigned variant codes which describe which of a set of possible variants of the subsystem exist within each genome (special codes expressing a total absence of the subsystem or remaining uncertainty exist). Construction of a large set of curated populated subsystems is at the center of the NMPDR and SEED annotation efforts. '''FIGfam''': FIGfams are protein families generated by the Fellowship for Interpretation of Genomes (FIG). These families are based on the collection of subsystems, as well as correspondences between genes in closely related strains (we describe the construction of FIGfams in a separate SOP). The important properties of these families are as follows: # Two PEGs which both occur within a single FIGfam are believed to have the same function. # There is a decision procedure associated with the family which can be invoked to determine whether or not a gene can be “safely” assigned the function associated with the family. '''Metabolic Reconstruction''': When we use the term metabolic reconstruction of a given genome we will simply mean the set of populated subsystems that contain the genome, the PEGs (and their assigned functions) that are connected to functional roles in these populated subsystems, and the specific variant code associated with the genome in each of the populated subsystems. '''NMPDR pathogen genome''': The NMPDR is responsible for five classes of genomes: # Campylobacter jejuni # Listeria monocytogenes # Staphylococcus aureus # Streptococcus pneumoniae and Streptococcus pyogenes # Pathogenic Vibrio We refer to these genomes as the NMPDR pathogens. The NMPDR carefully annotates some close relatives of these classes to provide accurate comparative context. Similarly, it includes a diverse collection of complete genomes that it annotates less accurately to provide context for comparative analysis. Now we can discuss what we mean by the annotations and the standard procedure for making those annotations. === The Annotation Procedure === The annotation of genomes begins after the genes have been identified and the genome has been integrated into a SEED environment. The annotation process then proceeds through the following steps: # Use of FIGfams # Use of Subsystems # Annotation of Prophages # Resolution of Conflicts # Improvement of Annotation Via New Subsystems # Continuous Refinement Via Analysis of Literature The following sections cover each of these steps in detail. We present the sequence of steps as commands issued from the command line. In fact, we are constructing a pipeline managed from a web interface that is intended to allow a relatively unskilled user to control the process. ==== Step 1: Use of FIGfams ==== For each new genome, we form a set of anticipated families by gathering all FIGfams with members in genomes from the same class. We begin the annotation by taking the anticipated families and searching for occurrences of these FIGfams within the new genome. This is achieved by invoking install_anticipated_functions User GenomeToBeAnnotated FileOfGenomesGivingContext Where User is the individual issuing the command, GenomeToBeAnnotated is the ID of the genome to be annotated (it is assumed that this genome has already been installed in the current SEED), and FileOfGenomesGivingContext is a file containing genome IDs (one per line) of the existing genomes from the same class. The effect of running this command will be to locate the instances of families when possible, to assign the appropriate function to the located genes, and to record detailed annotations of which FIGfam families were used as the basis for each annotation (along with the User and timestamps). ==== Step 2: Use of Subsystems ==== Once initial assignments based on FIGfams has been accomplished, it is possible to rapidly assess the presence and absence of subsystems (it is worth noting that every functional role within existing subsystems is covered by a FIGfam). The process begins with potentially_missed_assignments GenomeToBeAnnotated FileOfGenomesGivingContext This command will produce a list of assignments that may have been missed. This list is formed by looking at subsystems contained in each of the genomes that make up the context, checking for subsystems in which a majority (but not all) of the genes have corresponding genes in the new genome, and candidates for the missing genes can be located. The tool produces a list of possibly missed assignments that must be checked by an annotator. Once the list of possibly missed assignments has been processed, the following command can be run: add_to_subsystems User GenomeToBeAnnotated FileOfGenomesGivingContext This command will compute the set of subsystems from the context genomes for which all of the corresponding genes can be located in the new genome. This set of subsystems will then be split into two lists: # Some of the subsystems are marked as automatically extendable by their curators. For these subsystems, the new genome will be added to the populated subsystem. # For those subsystems that are not marked as automatically extendable, the fact that the new genome should be added to the subsystem will be recorded. Curators for these subsystems will be notified and asked to add the new genome. The tentative metabolic reconstruction is formed (including subsystems from both lists). ==== Step 3: Annotation of Prophages and Mobil Elements ==== For each class of NMPDR pathogen we maintain as features a list of prophages and other mobil elements. Execution of mark_features prophage User GenomeToBeAnnotated FileOfGenomesGivingContext mark_features mobil_element User GenomeToBeAnnotated FileOfGenomesGivingContext will cause instances of these prohages and other mobile elements to be detected and marked as features in the new genome. These annotations will be logged. ==== Step 4: Resolution of Conflicts ==== FIGfams are not always annotated consistently. This can happen in cases in which it is possible to assert that a set of genes have a common function, but for which disagreement remains about exactly how to label the role played by members of the family. In such cases, a functional role is associated with the FIGfam, but individual members of the family may have distinct (inconsistent) functions. The number of such instances is gradually dropping, but we have adopted the position that it is better to retain the inconsistency (reflecting real uncertainty) rather than enforcing a common function. Execution of the following command will produce a list of conflicts that should be examined by an annotator: potential_conflicts GenomeToBeAnnotated FileOfGenomesGivingContext ==== Step 5: Improvement of Annotation Via New Subsystems ==== Normal subsystem maintenance occurs constantly. The basic activity of our annotators is to extend existing subsystems and to define and populate new subsystems. These activities produce a gradual improvement in the quality of annotations for all genomes. All new annotations are logged as they are made. ==== Step 6: Continuous Refinement Via Analysis of Literature ==== Annotators should continuously review new literature, seeking cases in which gene functions can be improved based on new results. Sometimes, this results in improvements in function for a specific gene (and these results are then propagated to other members of the NMPDR pathogen class). More often, these new results are used as the basis for new subsystems and have a broader impact. 32d8ced619a1f77d5557272e1151dfe699db2e24 1475 1472 2006-08-23T15:46:57Z RossOverbeek 12 wikitext text/x-wiki == Annotation of Genomes: == === Standard Operating Procedure === === Introduction === This procedure describes the annotation process used by the SEED and NMPDR annotators and curators. Let us begin by discussing a number of terms that we use in this document: '''Functional Role''': The concept of functional role is both basic and primitive in the sense that we will not pretend to offer a precise definition. It corresponds roughly to a single logical role that a gene or gene product may play in the operation of a cell. '''Gene function''': The function of a protein-encoding gene (PEG) is the functional role played by the product of the gene or an expression describing a set of roles played by the encoded protein. The operators used to construct expressions and the meanings associated with the operators are described in http://www.nmpdr.org/FIG/Html/SEED_functions.html Genes other than PEGs can also be assigned functions (e.g., SSU rRNA). However, in most cases the functions assigned to genes other than PEGs tend not to be problematic. This document will focus solely on annotation of PEGs. '''Assigning a gene function and annotation''': Annotators assign gene functions to genes, and we call this process annotation. In most contexts, people use the term annotation to refer to assignments of function to the genes within a single organism. We certainly use the term in this sense, but we also use it to describe the process of assigning functions to corresponding genes from numerous genomes. Our basic approach to annotation is to ask our annotators to annotate the genes included in a subsystem (e.g., glycolysis) across all genomes. This process of annotation of the genes within a subsystem across a set of genomes, rather than annotation of genes within a single genome, allows our annotators to focus on a constrained set of functional roles and attempt to accurately identify exactly what variant, if any, of a subsystem exists in each of the genomes. We use the term annotation to refer to assigning functions to genes (either within a single organism or to a constrained set of gene/protein families across a set of organisms). This activity certainly is closely related to the construction of subsystems and protein families (which we call FIGfams), but we will describe those activities elsewhere. '''Subsystem''': A subsystem is a set of functional roles that an annotator has decided should be thought of as related. Frequently, subsystems represent the collection of functional roles that make up a metabolic pathway, a complex (e.g., the ribosome), or a class of proteins (e.g., two-component signal-transduction proteins within Staphylococcus aureus). A populated subsystem is a subsystem with an attached spreadsheet. The rows of the spreadsheet represent genomes and the columns represent the functional roles of the spreadsheet. Each cell contains the identifiers of genes from the corresponding genome the implement the specific functional role. That is, a populated subsystem specifies which genes implement instances of the subsystem in each of the genomes. The rows of a populated genome are assigned variant codes which describe which of a set of possible variants of the subsystem exist within each genome (special codes expressing a total absence of the subsystem or remaining uncertainty exist). Construction of a large set of curated populated subsystems is at the center of the NMPDR and SEED annotation efforts. '''FIGfam''': FIGfams are protein families generated by the Fellowship for Interpretation of Genomes (FIG). These families are based on the collection of subsystems, as well as correspondences between genes in closely related strains (we describe the construction of FIGfams in a separate SOP). The important properties of these families are as follows: # Two PEGs which both occur within a single FIGfam are believed to have the same function. # There is a decision procedure associated with the family which can be invoked to determine whether or not a gene can be “safely” assigned the function associated with the family. '''Metabolic Reconstruction''': When we use the term metabolic reconstruction of a given genome we will simply mean the set of populated subsystems that contain the genome, the PEGs (and their assigned functions) that are connected to functional roles in these populated subsystems, and the specific variant code associated with the genome in each of the populated subsystems. '''NMPDR pathogen genome''': The NMPDR is responsible for five classes of genomes: # Campylobacter jejuni # Listeria monocytogenes # Staphylococcus aureus # Streptococcus pneumoniae and Streptococcus pyogenes # Pathogenic Vibrio We refer to these genomes as the NMPDR pathogens. The NMPDR carefully annotates some close relatives of these classes to provide accurate comparative context. Similarly, it includes a diverse collection of complete genomes that it annotates less accurately to provide context for comparative analysis. Now we can discuss what we mean by the annotations and the standard procedure for making those annotations. === The Annotation Procedure === The annotation of genomes begins after the genes have been identified and the genome has been integrated into a SEED environment. The annotation process then proceeds through the following steps: # Use of FIGfams # Use of Subsystems # Annotation of Prophages # Resolution of Conflicts # Improvement of Annotation Via New Subsystems # Continuous Refinement Via Analysis of Literature The following sections cover each of these steps in detail. We present the sequence of steps as commands issued from the command line. In fact, we are constructing a pipeline managed from a web interface that is intended to allow a relatively unskilled user to control the process. ==== Step 1: Use of FIGfams ==== For each new genome, we form a set of anticipated families by gathering all FIGfams with members in genomes from the same class. We begin the annotation by taking the anticipated families and searching for occurrences of these FIGfams within the new genome. This is achieved by invoking install_anticipated_functions User GenomeToBeAnnotated FileOfGenomesGivingContext Where User is the individual issuing the command, GenomeToBeAnnotated is the ID of the genome to be annotated (it is assumed that this genome has already been installed in the current SEED), and FileOfGenomesGivingContext is a file containing genome IDs (one per line) of the existing genomes from the same class. The effect of running this command will be to locate the instances of families when possible, to assign the appropriate function to the located genes, and to record detailed annotations of which FIGfam families were used as the basis for each annotation (along with the User and timestamps). ==== Step 2: Use of Subsystems ==== Once initial assignments based on FIGfams has been accomplished, it is possible to rapidly assess the presence and absence of subsystems (it is worth noting that every functional role within existing subsystems is covered by a FIGfam). The process begins with potentially_missed_assignments User GenomeToBeAnnotated FileOfGenomesGivingContext This command will produce a list of assignments that may have been missed. This list is formed by looking at subsystems contained in each of the genomes that make up the context, checking for subsystems in which a majority (but not all) of the genes have corresponding genes in the new genome, and candidates for the missing genes can be located. The tool produces a list of possibly missed assignments that must be checked by an annotator. The assignments are installed as an assignment set for the given User. Once the list of possibly missed assignments has been processed, the following command can be run: add_to_subsystems User GenomeToBeAnnotated FileOfGenomesGivingContext This command will compute the set of subsystems from the context genomes for which all of the corresponding genes can be located in the new genome. This set of subsystems will then be split into two lists: # Some of the subsystems are marked as automatically extendable by their curators. For these subsystems, the new genome will be added to the populated subsystem. # For those subsystems that are not marked as automatically extendable, the fact that the new genome should be added to the subsystem will be recorded. Curators for these subsystems will be notified and asked to add the new genome. The tentative metabolic reconstruction is formed (including subsystems from both lists). ==== Step 3: Annotation of Prophages and Mobil Elements ==== For each class of NMPDR pathogen we maintain as features a list of prophages and other mobil elements. Execution of mark_features prophage User GenomeToBeAnnotated FileOfGenomesGivingContext mark_features mobil_element User GenomeToBeAnnotated FileOfGenomesGivingContext will cause instances of these prohages and other mobile elements to be detected and marked as features in the new genome. These annotations will be logged. ==== Step 4: Resolution of Conflicts ==== FIGfams are not always annotated consistently. This can happen in cases in which it is possible to assert that a set of genes have a common function, but for which disagreement remains about exactly how to label the role played by members of the family. In such cases, a functional role is associated with the FIGfam, but individual members of the family may have distinct (inconsistent) functions. The number of such instances is gradually dropping, but we have adopted the position that it is better to retain the inconsistency (reflecting real uncertainty) rather than enforcing a common function. Execution of the following command will produce a list of conflicts that should be examined by an annotator: potential_conflicts GenomeToBeAnnotated FileOfGenomesGivingContext ==== Step 5: Improvement of Annotation Via New Subsystems ==== Normal subsystem maintenance occurs constantly. The basic activity of our annotators is to extend existing subsystems and to define and populate new subsystems. These activities produce a gradual improvement in the quality of annotations for all genomes. All new annotations are logged as they are made. ==== Step 6: Continuous Refinement Via Analysis of Literature ==== Annotators should continuously review new literature, seeking cases in which gene functions can be improved based on new results. Sometimes, this results in improvements in function for a specific gene (and these results are then propagated to other members of the NMPDR pathogen class). More often, these new results are used as the basis for new subsystems and have a broader impact. ed6ff58731f60b28315ce8c306a0a50756ab5244 1479 1475 2006-08-26T21:52:03Z RossOverbeek 12 /* Step 3: Annotation of Prophages and Mobil Elements */ wikitext text/x-wiki == Annotation of Genomes: == === Standard Operating Procedure === === Introduction === This procedure describes the annotation process used by the SEED and NMPDR annotators and curators. Let us begin by discussing a number of terms that we use in this document: '''Functional Role''': The concept of functional role is both basic and primitive in the sense that we will not pretend to offer a precise definition. It corresponds roughly to a single logical role that a gene or gene product may play in the operation of a cell. '''Gene function''': The function of a protein-encoding gene (PEG) is the functional role played by the product of the gene or an expression describing a set of roles played by the encoded protein. The operators used to construct expressions and the meanings associated with the operators are described in http://www.nmpdr.org/FIG/Html/SEED_functions.html Genes other than PEGs can also be assigned functions (e.g., SSU rRNA). However, in most cases the functions assigned to genes other than PEGs tend not to be problematic. This document will focus solely on annotation of PEGs. '''Assigning a gene function and annotation''': Annotators assign gene functions to genes, and we call this process annotation. In most contexts, people use the term annotation to refer to assignments of function to the genes within a single organism. We certainly use the term in this sense, but we also use it to describe the process of assigning functions to corresponding genes from numerous genomes. Our basic approach to annotation is to ask our annotators to annotate the genes included in a subsystem (e.g., glycolysis) across all genomes. This process of annotation of the genes within a subsystem across a set of genomes, rather than annotation of genes within a single genome, allows our annotators to focus on a constrained set of functional roles and attempt to accurately identify exactly what variant, if any, of a subsystem exists in each of the genomes. We use the term annotation to refer to assigning functions to genes (either within a single organism or to a constrained set of gene/protein families across a set of organisms). This activity certainly is closely related to the construction of subsystems and protein families (which we call FIGfams), but we will describe those activities elsewhere. '''Subsystem''': A subsystem is a set of functional roles that an annotator has decided should be thought of as related. Frequently, subsystems represent the collection of functional roles that make up a metabolic pathway, a complex (e.g., the ribosome), or a class of proteins (e.g., two-component signal-transduction proteins within Staphylococcus aureus). A populated subsystem is a subsystem with an attached spreadsheet. The rows of the spreadsheet represent genomes and the columns represent the functional roles of the spreadsheet. Each cell contains the identifiers of genes from the corresponding genome the implement the specific functional role. That is, a populated subsystem specifies which genes implement instances of the subsystem in each of the genomes. The rows of a populated genome are assigned variant codes which describe which of a set of possible variants of the subsystem exist within each genome (special codes expressing a total absence of the subsystem or remaining uncertainty exist). Construction of a large set of curated populated subsystems is at the center of the NMPDR and SEED annotation efforts. '''FIGfam''': FIGfams are protein families generated by the Fellowship for Interpretation of Genomes (FIG). These families are based on the collection of subsystems, as well as correspondences between genes in closely related strains (we describe the construction of FIGfams in a separate SOP). The important properties of these families are as follows: # Two PEGs which both occur within a single FIGfam are believed to have the same function. # There is a decision procedure associated with the family which can be invoked to determine whether or not a gene can be “safely” assigned the function associated with the family. '''Metabolic Reconstruction''': When we use the term metabolic reconstruction of a given genome we will simply mean the set of populated subsystems that contain the genome, the PEGs (and their assigned functions) that are connected to functional roles in these populated subsystems, and the specific variant code associated with the genome in each of the populated subsystems. '''NMPDR pathogen genome''': The NMPDR is responsible for five classes of genomes: # Campylobacter jejuni # Listeria monocytogenes # Staphylococcus aureus # Streptococcus pneumoniae and Streptococcus pyogenes # Pathogenic Vibrio We refer to these genomes as the NMPDR pathogens. The NMPDR carefully annotates some close relatives of these classes to provide accurate comparative context. Similarly, it includes a diverse collection of complete genomes that it annotates less accurately to provide context for comparative analysis. Now we can discuss what we mean by the annotations and the standard procedure for making those annotations. === The Annotation Procedure === The annotation of genomes begins after the genes have been identified and the genome has been integrated into a SEED environment. The annotation process then proceeds through the following steps: # Use of FIGfams # Use of Subsystems # Annotation of Prophages # Resolution of Conflicts # Improvement of Annotation Via New Subsystems # Continuous Refinement Via Analysis of Literature The following sections cover each of these steps in detail. We present the sequence of steps as commands issued from the command line. In fact, we are constructing a pipeline managed from a web interface that is intended to allow a relatively unskilled user to control the process. ==== Step 1: Use of FIGfams ==== For each new genome, we form a set of anticipated families by gathering all FIGfams with members in genomes from the same class. We begin the annotation by taking the anticipated families and searching for occurrences of these FIGfams within the new genome. This is achieved by invoking install_anticipated_functions User GenomeToBeAnnotated FileOfGenomesGivingContext Where User is the individual issuing the command, GenomeToBeAnnotated is the ID of the genome to be annotated (it is assumed that this genome has already been installed in the current SEED), and FileOfGenomesGivingContext is a file containing genome IDs (one per line) of the existing genomes from the same class. The effect of running this command will be to locate the instances of families when possible, to assign the appropriate function to the located genes, and to record detailed annotations of which FIGfam families were used as the basis for each annotation (along with the User and timestamps). ==== Step 2: Use of Subsystems ==== Once initial assignments based on FIGfams has been accomplished, it is possible to rapidly assess the presence and absence of subsystems (it is worth noting that every functional role within existing subsystems is covered by a FIGfam). The process begins with potentially_missed_assignments User GenomeToBeAnnotated FileOfGenomesGivingContext This command will produce a list of assignments that may have been missed. This list is formed by looking at subsystems contained in each of the genomes that make up the context, checking for subsystems in which a majority (but not all) of the genes have corresponding genes in the new genome, and candidates for the missing genes can be located. The tool produces a list of possibly missed assignments that must be checked by an annotator. The assignments are installed as an assignment set for the given User. Once the list of possibly missed assignments has been processed, the following command can be run: add_to_subsystems User GenomeToBeAnnotated FileOfGenomesGivingContext This command will compute the set of subsystems from the context genomes for which all of the corresponding genes can be located in the new genome. This set of subsystems will then be split into two lists: # Some of the subsystems are marked as automatically extendable by their curators. For these subsystems, the new genome will be added to the populated subsystem. # For those subsystems that are not marked as automatically extendable, the fact that the new genome should be added to the subsystem will be recorded. Curators for these subsystems will be notified and asked to add the new genome. The tentative metabolic reconstruction is formed (including subsystems from both lists). ==== Step 4: Resolution of Conflicts ==== FIGfams are not always annotated consistently. This can happen in cases in which it is possible to assert that a set of genes have a common function, but for which disagreement remains about exactly how to label the role played by members of the family. In such cases, a functional role is associated with the FIGfam, but individual members of the family may have distinct (inconsistent) functions. The number of such instances is gradually dropping, but we have adopted the position that it is better to retain the inconsistency (reflecting real uncertainty) rather than enforcing a common function. Execution of the following command will produce a list of conflicts that should be examined by an annotator: potential_conflicts GenomeToBeAnnotated FileOfGenomesGivingContext ==== Step 5: Improvement of Annotation Via New Subsystems ==== Normal subsystem maintenance occurs constantly. The basic activity of our annotators is to extend existing subsystems and to define and populate new subsystems. These activities produce a gradual improvement in the quality of annotations for all genomes. All new annotations are logged as they are made. ==== Step 6: Continuous Refinement Via Analysis of Literature ==== Annotators should continuously review new literature, seeking cases in which gene functions can be improved based on new results. Sometimes, this results in improvements in function for a specific gene (and these results are then propagated to other members of the NMPDR pathogen class). More often, these new results are used as the basis for new subsystems and have a broader impact. b44f4394c73eb6407a939d11c4f47e91b7e2cd67 1480 1479 2006-08-26T21:52:33Z RossOverbeek 12 /* Step 4: Resolution of Conflicts */ wikitext text/x-wiki == Annotation of Genomes: == === Standard Operating Procedure === === Introduction === This procedure describes the annotation process used by the SEED and NMPDR annotators and curators. Let us begin by discussing a number of terms that we use in this document: '''Functional Role''': The concept of functional role is both basic and primitive in the sense that we will not pretend to offer a precise definition. It corresponds roughly to a single logical role that a gene or gene product may play in the operation of a cell. '''Gene function''': The function of a protein-encoding gene (PEG) is the functional role played by the product of the gene or an expression describing a set of roles played by the encoded protein. The operators used to construct expressions and the meanings associated with the operators are described in http://www.nmpdr.org/FIG/Html/SEED_functions.html Genes other than PEGs can also be assigned functions (e.g., SSU rRNA). However, in most cases the functions assigned to genes other than PEGs tend not to be problematic. This document will focus solely on annotation of PEGs. '''Assigning a gene function and annotation''': Annotators assign gene functions to genes, and we call this process annotation. In most contexts, people use the term annotation to refer to assignments of function to the genes within a single organism. We certainly use the term in this sense, but we also use it to describe the process of assigning functions to corresponding genes from numerous genomes. Our basic approach to annotation is to ask our annotators to annotate the genes included in a subsystem (e.g., glycolysis) across all genomes. This process of annotation of the genes within a subsystem across a set of genomes, rather than annotation of genes within a single genome, allows our annotators to focus on a constrained set of functional roles and attempt to accurately identify exactly what variant, if any, of a subsystem exists in each of the genomes. We use the term annotation to refer to assigning functions to genes (either within a single organism or to a constrained set of gene/protein families across a set of organisms). This activity certainly is closely related to the construction of subsystems and protein families (which we call FIGfams), but we will describe those activities elsewhere. '''Subsystem''': A subsystem is a set of functional roles that an annotator has decided should be thought of as related. Frequently, subsystems represent the collection of functional roles that make up a metabolic pathway, a complex (e.g., the ribosome), or a class of proteins (e.g., two-component signal-transduction proteins within Staphylococcus aureus). A populated subsystem is a subsystem with an attached spreadsheet. The rows of the spreadsheet represent genomes and the columns represent the functional roles of the spreadsheet. Each cell contains the identifiers of genes from the corresponding genome the implement the specific functional role. That is, a populated subsystem specifies which genes implement instances of the subsystem in each of the genomes. The rows of a populated genome are assigned variant codes which describe which of a set of possible variants of the subsystem exist within each genome (special codes expressing a total absence of the subsystem or remaining uncertainty exist). Construction of a large set of curated populated subsystems is at the center of the NMPDR and SEED annotation efforts. '''FIGfam''': FIGfams are protein families generated by the Fellowship for Interpretation of Genomes (FIG). These families are based on the collection of subsystems, as well as correspondences between genes in closely related strains (we describe the construction of FIGfams in a separate SOP). The important properties of these families are as follows: # Two PEGs which both occur within a single FIGfam are believed to have the same function. # There is a decision procedure associated with the family which can be invoked to determine whether or not a gene can be “safely” assigned the function associated with the family. '''Metabolic Reconstruction''': When we use the term metabolic reconstruction of a given genome we will simply mean the set of populated subsystems that contain the genome, the PEGs (and their assigned functions) that are connected to functional roles in these populated subsystems, and the specific variant code associated with the genome in each of the populated subsystems. '''NMPDR pathogen genome''': The NMPDR is responsible for five classes of genomes: # Campylobacter jejuni # Listeria monocytogenes # Staphylococcus aureus # Streptococcus pneumoniae and Streptococcus pyogenes # Pathogenic Vibrio We refer to these genomes as the NMPDR pathogens. The NMPDR carefully annotates some close relatives of these classes to provide accurate comparative context. Similarly, it includes a diverse collection of complete genomes that it annotates less accurately to provide context for comparative analysis. Now we can discuss what we mean by the annotations and the standard procedure for making those annotations. === The Annotation Procedure === The annotation of genomes begins after the genes have been identified and the genome has been integrated into a SEED environment. The annotation process then proceeds through the following steps: # Use of FIGfams # Use of Subsystems # Annotation of Prophages # Resolution of Conflicts # Improvement of Annotation Via New Subsystems # Continuous Refinement Via Analysis of Literature The following sections cover each of these steps in detail. We present the sequence of steps as commands issued from the command line. In fact, we are constructing a pipeline managed from a web interface that is intended to allow a relatively unskilled user to control the process. ==== Step 1: Use of FIGfams ==== For each new genome, we form a set of anticipated families by gathering all FIGfams with members in genomes from the same class. We begin the annotation by taking the anticipated families and searching for occurrences of these FIGfams within the new genome. This is achieved by invoking install_anticipated_functions User GenomeToBeAnnotated FileOfGenomesGivingContext Where User is the individual issuing the command, GenomeToBeAnnotated is the ID of the genome to be annotated (it is assumed that this genome has already been installed in the current SEED), and FileOfGenomesGivingContext is a file containing genome IDs (one per line) of the existing genomes from the same class. The effect of running this command will be to locate the instances of families when possible, to assign the appropriate function to the located genes, and to record detailed annotations of which FIGfam families were used as the basis for each annotation (along with the User and timestamps). ==== Step 2: Use of Subsystems ==== Once initial assignments based on FIGfams has been accomplished, it is possible to rapidly assess the presence and absence of subsystems (it is worth noting that every functional role within existing subsystems is covered by a FIGfam). The process begins with potentially_missed_assignments User GenomeToBeAnnotated FileOfGenomesGivingContext This command will produce a list of assignments that may have been missed. This list is formed by looking at subsystems contained in each of the genomes that make up the context, checking for subsystems in which a majority (but not all) of the genes have corresponding genes in the new genome, and candidates for the missing genes can be located. The tool produces a list of possibly missed assignments that must be checked by an annotator. The assignments are installed as an assignment set for the given User. Once the list of possibly missed assignments has been processed, the following command can be run: add_to_subsystems User GenomeToBeAnnotated FileOfGenomesGivingContext This command will compute the set of subsystems from the context genomes for which all of the corresponding genes can be located in the new genome. This set of subsystems will then be split into two lists: # Some of the subsystems are marked as automatically extendable by their curators. For these subsystems, the new genome will be added to the populated subsystem. # For those subsystems that are not marked as automatically extendable, the fact that the new genome should be added to the subsystem will be recorded. Curators for these subsystems will be notified and asked to add the new genome. The tentative metabolic reconstruction is formed (including subsystems from both lists). ==== Step 3: Resolution of Conflicts ==== FIGfams are not always annotated consistently. This can happen in cases in which it is possible to assert that a set of genes have a common function, but for which disagreement remains about exactly how to label the role played by members of the family. In such cases, a functional role is associated with the FIGfam, but individual members of the family may have distinct (inconsistent) functions. The number of such instances is gradually dropping, but we have adopted the position that it is better to retain the inconsistency (reflecting real uncertainty) rather than enforcing a common function. Execution of the following command will produce a list of conflicts that should be examined by an annotator: potential_conflicts GenomeToBeAnnotated FileOfGenomesGivingContext ==== Step 5: Improvement of Annotation Via New Subsystems ==== Normal subsystem maintenance occurs constantly. The basic activity of our annotators is to extend existing subsystems and to define and populate new subsystems. These activities produce a gradual improvement in the quality of annotations for all genomes. All new annotations are logged as they are made. ==== Step 6: Continuous Refinement Via Analysis of Literature ==== Annotators should continuously review new literature, seeking cases in which gene functions can be improved based on new results. Sometimes, this results in improvements in function for a specific gene (and these results are then propagated to other members of the NMPDR pathogen class). More often, these new results are used as the basis for new subsystems and have a broader impact. e6667cb798845a896f64e790367f9a9cd782f47c 1481 1480 2006-08-26T21:52:50Z RossOverbeek 12 /* Step 5: Improvement of Annotation Via New Subsystems */ wikitext text/x-wiki == Annotation of Genomes: == === Standard Operating Procedure === === Introduction === This procedure describes the annotation process used by the SEED and NMPDR annotators and curators. Let us begin by discussing a number of terms that we use in this document: '''Functional Role''': The concept of functional role is both basic and primitive in the sense that we will not pretend to offer a precise definition. It corresponds roughly to a single logical role that a gene or gene product may play in the operation of a cell. '''Gene function''': The function of a protein-encoding gene (PEG) is the functional role played by the product of the gene or an expression describing a set of roles played by the encoded protein. The operators used to construct expressions and the meanings associated with the operators are described in http://www.nmpdr.org/FIG/Html/SEED_functions.html Genes other than PEGs can also be assigned functions (e.g., SSU rRNA). However, in most cases the functions assigned to genes other than PEGs tend not to be problematic. This document will focus solely on annotation of PEGs. '''Assigning a gene function and annotation''': Annotators assign gene functions to genes, and we call this process annotation. In most contexts, people use the term annotation to refer to assignments of function to the genes within a single organism. We certainly use the term in this sense, but we also use it to describe the process of assigning functions to corresponding genes from numerous genomes. Our basic approach to annotation is to ask our annotators to annotate the genes included in a subsystem (e.g., glycolysis) across all genomes. This process of annotation of the genes within a subsystem across a set of genomes, rather than annotation of genes within a single genome, allows our annotators to focus on a constrained set of functional roles and attempt to accurately identify exactly what variant, if any, of a subsystem exists in each of the genomes. We use the term annotation to refer to assigning functions to genes (either within a single organism or to a constrained set of gene/protein families across a set of organisms). This activity certainly is closely related to the construction of subsystems and protein families (which we call FIGfams), but we will describe those activities elsewhere. '''Subsystem''': A subsystem is a set of functional roles that an annotator has decided should be thought of as related. Frequently, subsystems represent the collection of functional roles that make up a metabolic pathway, a complex (e.g., the ribosome), or a class of proteins (e.g., two-component signal-transduction proteins within Staphylococcus aureus). A populated subsystem is a subsystem with an attached spreadsheet. The rows of the spreadsheet represent genomes and the columns represent the functional roles of the spreadsheet. Each cell contains the identifiers of genes from the corresponding genome the implement the specific functional role. That is, a populated subsystem specifies which genes implement instances of the subsystem in each of the genomes. The rows of a populated genome are assigned variant codes which describe which of a set of possible variants of the subsystem exist within each genome (special codes expressing a total absence of the subsystem or remaining uncertainty exist). Construction of a large set of curated populated subsystems is at the center of the NMPDR and SEED annotation efforts. '''FIGfam''': FIGfams are protein families generated by the Fellowship for Interpretation of Genomes (FIG). These families are based on the collection of subsystems, as well as correspondences between genes in closely related strains (we describe the construction of FIGfams in a separate SOP). The important properties of these families are as follows: # Two PEGs which both occur within a single FIGfam are believed to have the same function. # There is a decision procedure associated with the family which can be invoked to determine whether or not a gene can be “safely” assigned the function associated with the family. '''Metabolic Reconstruction''': When we use the term metabolic reconstruction of a given genome we will simply mean the set of populated subsystems that contain the genome, the PEGs (and their assigned functions) that are connected to functional roles in these populated subsystems, and the specific variant code associated with the genome in each of the populated subsystems. '''NMPDR pathogen genome''': The NMPDR is responsible for five classes of genomes: # Campylobacter jejuni # Listeria monocytogenes # Staphylococcus aureus # Streptococcus pneumoniae and Streptococcus pyogenes # Pathogenic Vibrio We refer to these genomes as the NMPDR pathogens. The NMPDR carefully annotates some close relatives of these classes to provide accurate comparative context. Similarly, it includes a diverse collection of complete genomes that it annotates less accurately to provide context for comparative analysis. Now we can discuss what we mean by the annotations and the standard procedure for making those annotations. === The Annotation Procedure === The annotation of genomes begins after the genes have been identified and the genome has been integrated into a SEED environment. The annotation process then proceeds through the following steps: # Use of FIGfams # Use of Subsystems # Annotation of Prophages # Resolution of Conflicts # Improvement of Annotation Via New Subsystems # Continuous Refinement Via Analysis of Literature The following sections cover each of these steps in detail. We present the sequence of steps as commands issued from the command line. In fact, we are constructing a pipeline managed from a web interface that is intended to allow a relatively unskilled user to control the process. ==== Step 1: Use of FIGfams ==== For each new genome, we form a set of anticipated families by gathering all FIGfams with members in genomes from the same class. We begin the annotation by taking the anticipated families and searching for occurrences of these FIGfams within the new genome. This is achieved by invoking install_anticipated_functions User GenomeToBeAnnotated FileOfGenomesGivingContext Where User is the individual issuing the command, GenomeToBeAnnotated is the ID of the genome to be annotated (it is assumed that this genome has already been installed in the current SEED), and FileOfGenomesGivingContext is a file containing genome IDs (one per line) of the existing genomes from the same class. The effect of running this command will be to locate the instances of families when possible, to assign the appropriate function to the located genes, and to record detailed annotations of which FIGfam families were used as the basis for each annotation (along with the User and timestamps). ==== Step 2: Use of Subsystems ==== Once initial assignments based on FIGfams has been accomplished, it is possible to rapidly assess the presence and absence of subsystems (it is worth noting that every functional role within existing subsystems is covered by a FIGfam). The process begins with potentially_missed_assignments User GenomeToBeAnnotated FileOfGenomesGivingContext This command will produce a list of assignments that may have been missed. This list is formed by looking at subsystems contained in each of the genomes that make up the context, checking for subsystems in which a majority (but not all) of the genes have corresponding genes in the new genome, and candidates for the missing genes can be located. The tool produces a list of possibly missed assignments that must be checked by an annotator. The assignments are installed as an assignment set for the given User. Once the list of possibly missed assignments has been processed, the following command can be run: add_to_subsystems User GenomeToBeAnnotated FileOfGenomesGivingContext This command will compute the set of subsystems from the context genomes for which all of the corresponding genes can be located in the new genome. This set of subsystems will then be split into two lists: # Some of the subsystems are marked as automatically extendable by their curators. For these subsystems, the new genome will be added to the populated subsystem. # For those subsystems that are not marked as automatically extendable, the fact that the new genome should be added to the subsystem will be recorded. Curators for these subsystems will be notified and asked to add the new genome. The tentative metabolic reconstruction is formed (including subsystems from both lists). ==== Step 3: Resolution of Conflicts ==== FIGfams are not always annotated consistently. This can happen in cases in which it is possible to assert that a set of genes have a common function, but for which disagreement remains about exactly how to label the role played by members of the family. In such cases, a functional role is associated with the FIGfam, but individual members of the family may have distinct (inconsistent) functions. The number of such instances is gradually dropping, but we have adopted the position that it is better to retain the inconsistency (reflecting real uncertainty) rather than enforcing a common function. Execution of the following command will produce a list of conflicts that should be examined by an annotator: potential_conflicts GenomeToBeAnnotated FileOfGenomesGivingContext ==== Step 4: Improvement of Annotation Via New Subsystems ==== Normal subsystem maintenance occurs constantly. The basic activity of our annotators is to extend existing subsystems and to define and populate new subsystems. These activities produce a gradual improvement in the quality of annotations for all genomes. All new annotations are logged as they are made. ==== Step 6: Continuous Refinement Via Analysis of Literature ==== Annotators should continuously review new literature, seeking cases in which gene functions can be improved based on new results. Sometimes, this results in improvements in function for a specific gene (and these results are then propagated to other members of the NMPDR pathogen class). More often, these new results are used as the basis for new subsystems and have a broader impact. 953909008bb0593f83506ed440e4b79d89663c57 1482 1481 2006-08-26T21:53:00Z RossOverbeek 12 /* Step 6: Continuous Refinement Via Analysis of Literature */ wikitext text/x-wiki == Annotation of Genomes: == === Standard Operating Procedure === === Introduction === This procedure describes the annotation process used by the SEED and NMPDR annotators and curators. Let us begin by discussing a number of terms that we use in this document: '''Functional Role''': The concept of functional role is both basic and primitive in the sense that we will not pretend to offer a precise definition. It corresponds roughly to a single logical role that a gene or gene product may play in the operation of a cell. '''Gene function''': The function of a protein-encoding gene (PEG) is the functional role played by the product of the gene or an expression describing a set of roles played by the encoded protein. The operators used to construct expressions and the meanings associated with the operators are described in http://www.nmpdr.org/FIG/Html/SEED_functions.html Genes other than PEGs can also be assigned functions (e.g., SSU rRNA). However, in most cases the functions assigned to genes other than PEGs tend not to be problematic. This document will focus solely on annotation of PEGs. '''Assigning a gene function and annotation''': Annotators assign gene functions to genes, and we call this process annotation. In most contexts, people use the term annotation to refer to assignments of function to the genes within a single organism. We certainly use the term in this sense, but we also use it to describe the process of assigning functions to corresponding genes from numerous genomes. Our basic approach to annotation is to ask our annotators to annotate the genes included in a subsystem (e.g., glycolysis) across all genomes. This process of annotation of the genes within a subsystem across a set of genomes, rather than annotation of genes within a single genome, allows our annotators to focus on a constrained set of functional roles and attempt to accurately identify exactly what variant, if any, of a subsystem exists in each of the genomes. We use the term annotation to refer to assigning functions to genes (either within a single organism or to a constrained set of gene/protein families across a set of organisms). This activity certainly is closely related to the construction of subsystems and protein families (which we call FIGfams), but we will describe those activities elsewhere. '''Subsystem''': A subsystem is a set of functional roles that an annotator has decided should be thought of as related. Frequently, subsystems represent the collection of functional roles that make up a metabolic pathway, a complex (e.g., the ribosome), or a class of proteins (e.g., two-component signal-transduction proteins within Staphylococcus aureus). A populated subsystem is a subsystem with an attached spreadsheet. The rows of the spreadsheet represent genomes and the columns represent the functional roles of the spreadsheet. Each cell contains the identifiers of genes from the corresponding genome the implement the specific functional role. That is, a populated subsystem specifies which genes implement instances of the subsystem in each of the genomes. The rows of a populated genome are assigned variant codes which describe which of a set of possible variants of the subsystem exist within each genome (special codes expressing a total absence of the subsystem or remaining uncertainty exist). Construction of a large set of curated populated subsystems is at the center of the NMPDR and SEED annotation efforts. '''FIGfam''': FIGfams are protein families generated by the Fellowship for Interpretation of Genomes (FIG). These families are based on the collection of subsystems, as well as correspondences between genes in closely related strains (we describe the construction of FIGfams in a separate SOP). The important properties of these families are as follows: # Two PEGs which both occur within a single FIGfam are believed to have the same function. # There is a decision procedure associated with the family which can be invoked to determine whether or not a gene can be “safely” assigned the function associated with the family. '''Metabolic Reconstruction''': When we use the term metabolic reconstruction of a given genome we will simply mean the set of populated subsystems that contain the genome, the PEGs (and their assigned functions) that are connected to functional roles in these populated subsystems, and the specific variant code associated with the genome in each of the populated subsystems. '''NMPDR pathogen genome''': The NMPDR is responsible for five classes of genomes: # Campylobacter jejuni # Listeria monocytogenes # Staphylococcus aureus # Streptococcus pneumoniae and Streptococcus pyogenes # Pathogenic Vibrio We refer to these genomes as the NMPDR pathogens. The NMPDR carefully annotates some close relatives of these classes to provide accurate comparative context. Similarly, it includes a diverse collection of complete genomes that it annotates less accurately to provide context for comparative analysis. Now we can discuss what we mean by the annotations and the standard procedure for making those annotations. === The Annotation Procedure === The annotation of genomes begins after the genes have been identified and the genome has been integrated into a SEED environment. The annotation process then proceeds through the following steps: # Use of FIGfams # Use of Subsystems # Annotation of Prophages # Resolution of Conflicts # Improvement of Annotation Via New Subsystems # Continuous Refinement Via Analysis of Literature The following sections cover each of these steps in detail. We present the sequence of steps as commands issued from the command line. In fact, we are constructing a pipeline managed from a web interface that is intended to allow a relatively unskilled user to control the process. ==== Step 1: Use of FIGfams ==== For each new genome, we form a set of anticipated families by gathering all FIGfams with members in genomes from the same class. We begin the annotation by taking the anticipated families and searching for occurrences of these FIGfams within the new genome. This is achieved by invoking install_anticipated_functions User GenomeToBeAnnotated FileOfGenomesGivingContext Where User is the individual issuing the command, GenomeToBeAnnotated is the ID of the genome to be annotated (it is assumed that this genome has already been installed in the current SEED), and FileOfGenomesGivingContext is a file containing genome IDs (one per line) of the existing genomes from the same class. The effect of running this command will be to locate the instances of families when possible, to assign the appropriate function to the located genes, and to record detailed annotations of which FIGfam families were used as the basis for each annotation (along with the User and timestamps). ==== Step 2: Use of Subsystems ==== Once initial assignments based on FIGfams has been accomplished, it is possible to rapidly assess the presence and absence of subsystems (it is worth noting that every functional role within existing subsystems is covered by a FIGfam). The process begins with potentially_missed_assignments User GenomeToBeAnnotated FileOfGenomesGivingContext This command will produce a list of assignments that may have been missed. This list is formed by looking at subsystems contained in each of the genomes that make up the context, checking for subsystems in which a majority (but not all) of the genes have corresponding genes in the new genome, and candidates for the missing genes can be located. The tool produces a list of possibly missed assignments that must be checked by an annotator. The assignments are installed as an assignment set for the given User. Once the list of possibly missed assignments has been processed, the following command can be run: add_to_subsystems User GenomeToBeAnnotated FileOfGenomesGivingContext This command will compute the set of subsystems from the context genomes for which all of the corresponding genes can be located in the new genome. This set of subsystems will then be split into two lists: # Some of the subsystems are marked as automatically extendable by their curators. For these subsystems, the new genome will be added to the populated subsystem. # For those subsystems that are not marked as automatically extendable, the fact that the new genome should be added to the subsystem will be recorded. Curators for these subsystems will be notified and asked to add the new genome. The tentative metabolic reconstruction is formed (including subsystems from both lists). ==== Step 3: Resolution of Conflicts ==== FIGfams are not always annotated consistently. This can happen in cases in which it is possible to assert that a set of genes have a common function, but for which disagreement remains about exactly how to label the role played by members of the family. In such cases, a functional role is associated with the FIGfam, but individual members of the family may have distinct (inconsistent) functions. The number of such instances is gradually dropping, but we have adopted the position that it is better to retain the inconsistency (reflecting real uncertainty) rather than enforcing a common function. Execution of the following command will produce a list of conflicts that should be examined by an annotator: potential_conflicts GenomeToBeAnnotated FileOfGenomesGivingContext ==== Step 4: Improvement of Annotation Via New Subsystems ==== Normal subsystem maintenance occurs constantly. The basic activity of our annotators is to extend existing subsystems and to define and populate new subsystems. These activities produce a gradual improvement in the quality of annotations for all genomes. All new annotations are logged as they are made. ==== Step 5: Continuous Refinement Via Analysis of Literature ==== Annotators should continuously review new literature, seeking cases in which gene functions can be improved based on new results. Sometimes, this results in improvements in function for a specific gene (and these results are then propagated to other members of the NMPDR pathogen class). More often, these new results are used as the basis for new subsystems and have a broader impact. d1e708c564be64aff23703dfddd3d14734e735a5 0 1381 1466 2006-08-13T23:12:22Z FolkerMeyer 2 [[Annotation of close strains]] moved to [[Annotation of close strain sets]] wikitext text/x-wiki #REDIRECT [[Annotation of close strain sets]] 2d9e0abd4ec04f0243aef7da591e36a53310b4cd 0 1371 1467 1462 2006-08-13T23:12:31Z VeronikaVonstein 6 wikitext text/x-wiki == SEED standard operating procedures == To generate data that is usefull to the various communities involved in the process of annotation and use of annotations, we make available out standard operating procedures. * [[GeneCalling|Gene calling]] * Annotation ** [[Annotation_of_close_strain_sets|Annotation of close strain sets]] ** Annotation of diverse genomes. 79db8d2dd71ee681a3ac4855773e86674666c33e 1470 1467 2006-08-14T18:51:19Z FolkerMeyer 2 wikitext text/x-wiki == SEED standard operating procedures == To generate data that is useful to the various communities involved in the process of annotation and use of annotations, we make available out standard operating procedures. * [[GeneCalling|Gene calling]] * Annotation ** [[Annotation_of_close_strain_sets|Annotation of close strain sets]] ** Annotation of diverse genomes. d8655210fd1c4ca85b3307c6f31331a247374ee7 8 1090 1468 1438 2006-08-13T23:14:33Z FolkerMeyer 2 wikitext text/x-wiki * navigation ** Home_of_the_SEED|Home of the SEED ** Annotating_1000_genomes|Manifesto ** SEED_People| SEED People ** Contact| Contact * SEEDs ** http://explorer.theseed.org/FIG/index.cgi|SEED-Viewer ** http://theseed.uchicago.edu/FIG/index.cgi|Trial-SEED * Help and other Materials ** DownloadPage|Software and Data Download Page ** Glossary|Glossary ** SOPs|Our Standard Operating Procedures ** misc|Miscellaneous Materials 4d35bc0d85e433cfc5c6296b7936a5474acf2873 1469 1468 2006-08-13T23:16:00Z FolkerMeyer 2 wikitext text/x-wiki * navigation ** Home_of_the_SEED|Home of the SEED ** Annotating_1000_genomes|Manifesto ** SEED_People| SEED People ** Contact| Contact * SEEDs ** http://explorer.theseed.org/FIG/index.cgi|SEED-Viewer ** http://theseed.uchicago.edu/FIG/index.cgi|Trial-SEED * Help and other Materials ** DownloadPage|Download Page ** Glossary|Glossary ** SOPs|SOPs ** misc|Miscellaneous Materials 9be1ce5458ed87e7fb6f3c31f7fe4a48857a785e 1476 1469 2006-08-23T21:05:23Z WilliamMihalo 3 wikitext text/x-wiki * navigation ** Home_of_the_SEED|Home of the SEED ** Annotating_1000_genomes|Manifesto ** SEED_People| SEED People ** Contact| Contact * SEEDs ** http://seed-viewer.theseed.org/FIG/index.cgi|SEED-Viewer ** http://theseed.uchicago.edu/FIG/index.cgi|Trial-SEED * Help and other Materials ** DownloadPage|Download Page ** Glossary|Glossary ** SOPs|SOPs ** misc|Miscellaneous Materials 1804bc68f9480fb17bed0bf6081d88b1a1fce7bd 1487 1476 2006-10-04T22:27:53Z BobOlson 5 wikitext text/x-wiki * navigation ** Home_of_the_SEED|Home of the SEED ** Annotating_1000_genomes|Manifesto ** SEED_People| SEED People ** Contact| Contact * SEEDs ** http://seed-viewer.theseed.org/FIG/index.cgi|SEED-Viewer ** http://theseed.uchicago.edu/FIG/index.cgi|Trial-SEED ** http://seed.sdsu.edu/FIG/index.cgi|Metagenomics SEED * Help and other Materials ** DownloadPage|Download Page ** Glossary|Glossary ** SOPs|SOPs ** misc|Miscellaneous Materials 4a80bb5a1a7309ab4d28a98c743c928dc1683e6e 1490 1487 2006-10-13T21:42:34Z DanielPaarmann 8 wikitext text/x-wiki * navigation ** Home_of_the_SEED|Home of the SEED ** Annotating_1000_genomes|Manifesto ** SEED_People| SEED People ** Contact| Contact * SEEDs ** http://seed-viewer.theseed.org/FIG/index.cgi|SEED-Viewer ** http://theseed.uchicago.edu/FIG/index.cgi|Trial-SEED ** http://seed.sdsu.edu/FIG/index.cgi|Metagenomics SEED * Help and other Materials ** DownloadPage|Download Page ** Glossary|Glossary ** SOPs|SOPs ** SpecialPurposeDBs|Special Purpose DBs 94685308ebec5eb9c386f65aeedfb03b69011bb8 1494 1490 2006-10-30T22:34:41Z FolkerMeyer 2 wikitext text/x-wiki * navigation ** Home_of_the_SEED|Home of the SEED ** Annotating_1000_genomes|Manifesto ** SEED_People| SEED People ** Contact| Contact * SEEDs ** http://seed-viewer.theseed.org/FIG/index.cgi|SEED-Viewer ** http://theseed.uchicago.edu/FIG/index.cgi|Trial-SEED ** http://seed.sdsu.edu/FIG/index.cgi|Metagenomics SEED * Miscellaneous ** DownloadPage|Download Page ** Glossary|Glossary ** SOPs|SOPs ** SpecialPurposeDBs|Special Purpose DBs 629d2578b0115feb7da17f80c7d336614f68f3b5 1495 1494 2006-10-31T15:06:53Z FolkerMeyer 2 included FAQ in menu bar wikitext text/x-wiki * navigation ** Home_of_the_SEED|Home of the SEED ** Annotating_1000_genomes|Manifesto ** SEED_People| SEED People ** Contact| Contact * SEEDs ** http://seed-viewer.theseed.org/FIG/index.cgi|SEED-Viewer ** http://theseed.uchicago.edu/FIG/index.cgi|Trial-SEED ** http://seed.sdsu.edu/FIG/index.cgi|Metagenomics SEED * Miscellaneous ** FAQ|FAQ ** DownloadPage|Download Page ** Glossary|Glossary ** SOPs|SOPs ** SpecialPurposeDBs|Special Purpose DBs b0c0b10f220b2057861ccc56c3d030cd7e4a6533 1496 1495 2006-10-31T16:11:27Z FolkerMeyer 2 wikitext text/x-wiki * navigation ** Home_of_the_SEED|Home of the SEED ** Annotating_1000_genomes|Manifesto ** SEED_People| SEED People ** Contact| Contact * SEEDs ** http://seed-viewer.theseed.org/FIG/index.cgi|SEED-Viewer ** http://theseed.uchicago.edu/FIG/index.cgi|Trial-SEED ** http://seed.sdsu.edu/FIG/index.cgi|Metagenomics SEED * Miscellaneous ** DownloadPage|Download Page ** Glossary|Glossary ** SOPs|SOPs ** SpecialPurposeDBs|Special Purpose DBs 629d2578b0115feb7da17f80c7d336614f68f3b5 0 1374 1471 1437 2006-08-16T15:48:22Z VeronikaVonstein 6 wikitext text/x-wiki The people behind SEED are the following: * [http://www.thefig.info FIG] ** Ross Overbeek ** Veronika Vonstein ** Gordon Pusch ** Bruce Parrello ** Rob Edwards ** Andrei Ostermann ** Michael Fonstein ** Svetlana Gerdes ** Olga Zagnitko ** Olga Vassieva ** ... * [http://www.mcs.anl.gov Mathematics and Computer Science Department] [http://www.anl.gov Argonne National Labs] ** Rick Stevens ** Terry Disz ** Robert Olson ** Kaitlyn Hwang ** Folker Meyer ** ... * [http://www.ci.uchicago.ed Computation Institure] [http://www.uchicago.edu University of Chicago] ** Michael Kubal ** Matt Cohoon ** Jen Zinner ** Daniela Bartels ** Tobias Paczian ** Andreas Wilke ** Daniel Paarmann ** William Mihalo ** ... * [http://www.uiuc.edu University of Illinois at Urbana-Champaign] ** Gary J. Olson ** Leslie McNeil * [http://www.hope-college.edu Hope College] ** Matt DeJongh ** Aaron Best * [http://www.utmem.edu/ University of Memphis Tennessee] ** Rami Aziz 4c3152e79200053af397815d51067f3fa71297c0 1486 1471 2006-08-31T13:41:51Z GordonPusch 13 "Institute" mispelled wikitext text/x-wiki The people behind SEED are the following: * [http://www.thefig.info FIG] ** Ross Overbeek ** Veronika Vonstein ** Gordon Pusch ** Bruce Parrello ** Rob Edwards ** Andrei Ostermann ** Michael Fonstein ** Svetlana Gerdes ** Olga Zagnitko ** Olga Vassieva ** ... * [http://www.mcs.anl.gov Mathematics and Computer Science Department] [http://www.anl.gov Argonne National Labs] ** Rick Stevens ** Terry Disz ** Robert Olson ** Kaitlyn Hwang ** Folker Meyer ** ... * [http://www.ci.uchicago.ed Computation Institute] [http://www.uchicago.edu University of Chicago] ** Michael Kubal ** Matt Cohoon ** Jen Zinner ** Daniela Bartels ** Tobias Paczian ** Andreas Wilke ** Daniel Paarmann ** William Mihalo ** ... * [http://www.uiuc.edu University of Illinois at Urbana-Champaign] ** Gary J. Olson ** Leslie McNeil * [http://www.hope-college.edu Hope College] ** Matt DeJongh ** Aaron Best * [http://www.utmem.edu/ University of Memphis Tennessee] ** Rami Aziz 2c307bc9b2be05257c48b315c42cabd5fb45e5f6 1512 1486 2006-11-01T22:20:51Z VeronikaVonstein 6 wikitext text/x-wiki The people behind SEED are the following: * [http://www.thefig.info FIG] ** Ross Overbeek ** Veronika Vonstein ** Gordon Pusch ** Bruce Parrello ** Rob Edwards ** Andrei Osterman ** Michael Fonstein ** Svetlana Gerdes ** Olga Zagnitko ** Olga Vassieva ** Yakov Kogan ** Irina Goltsman * [http://www.mcs.anl.gov Mathematics and Computer Science Department] [http://www.anl.gov Argonne National Labs] ** Rick Stevens ** Terry Disz ** Robert Olson ** Kaitlyn Hwang ** Folker Meyer ** ... * [http://www.ci.uchicago.ed Computation Institute] [http://www.uchicago.edu University of Chicago] ** Michael Kubal ** Matt Cohoon ** Jen Zinner ** Daniela Bartels ** Tobias Paczian ** Andreas Wilke ** Daniel Paarmann ** William Mihalo ** ... * [http://www.uiuc.edu University of Illinois at Urbana-Champaign] ** Gary J. Olson ** Leslie McNeil * [http://www.hope-college.edu Hope College] ** Matt DeJongh ** Aaron Best * [http://www.utmem.edu/ University of Memphis Tennessee] ** Rami Aziz 23c6d22f098579bb28b19482e8271ecddfa846da 0 1376 1473 1423 2006-08-16T18:03:28Z FolkerMeyer 2 wikitext text/x-wiki There are numerous pages with information on the SEED floating around. This page attempts to collect links to them * [http://www-unix.mcs.anl.gov/SEEDWiki/ SEED installation Wiki] * [http://www.theseed.org/SubsystemPaperSupplementalMaterial/index.html Supplementary material for the NAR Subsystem Paper] 72c1687765e4cb1ce3c03b5b21d7b77d0dee741e 0 1 1474 1427 2006-08-16T18:05:12Z FolkerMeyer 2 wikitext text/x-wiki With the growing number of genomes becoming available, a software environment is needed to produce accurate and consistent annotations. The SEED is that environment. We provide a public [http://explorer.theseed.org/FIG/index.cgi SEED-Viewer] that allows read-only access to the latest data and annotations. For users interested in editing and learning how to use the system, we also provide a [http://theseed.uchicago.edu/FIG/index.cgi Trial-SEED]. As described in our [[Annotating_1000_genomes|manifesto]] the [[Glossary#annotation|annotation]] is not performed on a gene by gene basis per genome, but rather by [[Glossary#subsystem|subsystem]] by an expert curator across many genomes at a time. We make all our software and data available for download and use on our [[DownloadPage]] page. * When using the SEED, please cite: Overbeek et al., [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16214803&query_hl=2&itool=pubmed_docsum|Nucleic Acids Res 33(17)], 2005 ([http://www.theseed.org/SubsystemPaperSupplementalMaterial/index.html Supplementary material]) * Our approaches to annotation, gene calling etc are outlined in a series of [[SOPs|Standard Operating Procedures]]. f12f13512d0530c1f776f5dfcbde7158e8246e27 1477 1474 2006-08-23T21:19:59Z WilliamMihalo 3 wikitext text/x-wiki With the growing number of genomes becoming available, a software environment is needed to produce accurate and consistent annotations. The SEED is that environment. We provide a public [http://seedviewer.theseed.org/FIG/index.cgi SEED-Viewer] that allows read-only access to the latest data and annotations. For users interested in editing and learning how to use the system, we also provide a [http://theseed.uchicago.edu/FIG/index.cgi Trial-SEED]. As described in our [[Annotating_1000_genomes|manifesto]] the [[Glossary#annotation|annotation]] is not performed on a gene by gene basis per genome, but rather by [[Glossary#subsystem|subsystem]] by an expert curator across many genomes at a time. We make all our software and data available for download and use on our [[DownloadPage]] page. * When using the SEED, please cite: Overbeek et al., [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16214803&query_hl=2&itool=pubmed_docsum|Nucleic Acids Res 33(17)], 2005 ([http://www.theseed.org/SubsystemPaperSupplementalMaterial/index.html Supplementary material]) * Our approaches to annotation, gene calling etc are outlined in a series of [[SOPs|Standard Operating Procedures]]. 604c15182c64f8b96f21d89eaff92e40934be815 1478 1477 2006-08-23T21:20:48Z WilliamMihalo 3 wikitext text/x-wiki With the growing number of genomes becoming available, a software environment is needed to produce accurate and consistent annotations. The SEED is that environment. We provide a public [http://seed-viewer.theseed.org/FIG/index.cgi SEED-Viewer] that allows read-only access to the latest data and annotations. For users interested in editing and learning how to use the system, we also provide a [http://theseed.uchicago.edu/FIG/index.cgi Trial-SEED]. As described in our [[Annotating_1000_genomes|manifesto]] the [[Glossary#annotation|annotation]] is not performed on a gene by gene basis per genome, but rather by [[Glossary#subsystem|subsystem]] by an expert curator across many genomes at a time. We make all our software and data available for download and use on our [[DownloadPage]] page. * When using the SEED, please cite: Overbeek et al., [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16214803&query_hl=2&itool=pubmed_docsum|Nucleic Acids Res 33(17)], 2005 ([http://www.theseed.org/SubsystemPaperSupplementalMaterial/index.html Supplementary material]) * Our approaches to annotation, gene calling etc are outlined in a series of [[SOPs|Standard Operating Procedures]]. a4620e20fee40bd8694d75b4ab47f3cb5f88249e 1488 1478 2006-10-13T19:43:31Z DanielPaarmann 8 wikitext text/x-wiki With the growing number of available genomes, the need for an environment to support effective comparative analysis increases. The original SEED Project was started at FIG as an open source effort. Argonne National Lab and the University of Chicago joined the project, and now much of the activity occurs at those two institutions (as well as the University of Illinois at Urbana-Champaign, Hope college, San Diego State University, the Burnham Institute and a number of other institutions). The cooperative effort focuses on the development of the annotation environment called the SEED and, more importantly, on the development of curated genomic data. We provide a public [http://seed-viewer.theseed.org/FIG/index.cgi SEED-Viewer] that allows read-only access to the latest data and annotations. For users interested in editing and learning how to use the system, we also provide a [http://theseed.uchicago.edu/FIG/index.cgi Trial-SEED]. As described in our [[Annotating_1000_genomes|manifesto]] the [[Glossary#annotation|annotation]] is not performed on a gene by gene basis per genome, but rather by [[Glossary#subsystem|subsystem]] by an expert curator across many genomes at a time. We make all our software and data available for download and use on our [[DownloadPage]] page. * When using the SEED, please cite: Overbeek et al., [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16214803&query_hl=2&itool=pubmed_docsum|Nucleic Acids Res 33(17)], 2005 ([http://www.theseed.org/SubsystemPaperSupplementalMaterial/index.html Supplementary material]) * Our approaches to annotation, gene calling etc are outlined in a series of [[SOPs|Standard Operating Procedures]]. 75755ce0ae4863002c38b51f2a3e0aa5851602ca 1489 1488 2006-10-13T19:49:58Z DanielPaarmann 8 wikitext text/x-wiki With the growing number of available genomes, the need for an environment to support effective comparative analysis increases. The original SEED Project was started by the [http://thefig.info Fellowship of Interpretation of Genomes (FIG)] as an open source effort. Argonne National Lab and the University of Chicago joined the project, and now much of the activity occurs at those two institutions (as well as the University of Illinois at Urbana-Champaign, Hope college, San Diego State University, the Burnham Institute and a number of other institutions). The cooperative effort focuses on the development of the annotation environment called the SEED and, more importantly, on the development of curated genomic data. We provide a public [http://seed-viewer.theseed.org/FIG/index.cgi SEED-Viewer] that allows read-only access to the latest data and annotations. For users interested in editing and learning how to use the system, we also provide a [http://theseed.uchicago.edu/FIG/index.cgi Trial-SEED]. As described in our [[Annotating_1000_genomes|manifesto]] the [[Glossary#annotation|annotation]] is not performed on a gene by gene basis per genome, but rather by [[Glossary#subsystem|subsystem]] by an expert curator across many genomes at a time. We make all our software and data available for download and use on our [[DownloadPage]] page. * When using the SEED, please cite: Overbeek et al., [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16214803&query_hl=2&itool=pubmed_docsum|Nucleic Acids Res 33(17)], 2005 ([http://www.theseed.org/SubsystemPaperSupplementalMaterial/index.html Supplementary material]) * Our approaches to annotation, gene calling etc are outlined in a series of [[SOPs|Standard Operating Procedures]]. a549f6c08b5d3c7eeaad6cf2d160e1f0ba5018ea 1492 1489 2006-10-27T14:45:58Z FolkerMeyer 2 wikitext text/x-wiki With the growing number of available genomes, the need for an environment to support effective comparative analysis increases. The original SEED Project was started by the [http://thefig.info Fellowship of Interpretation of Genomes (FIG)] as an open source effort. Argonne National Lab and the University of Chicago joined the project, and now much of the activity occurs at those two institutions (as well as the University of Illinois at Urbana-Champaign, Hope college, San Diego State University, the Burnham Institute and a number of other institutions). The cooperative effort focuses on the development of the annotation environment called the SEED and, more importantly, on the development of curated genomic data. We provide a public [http://seed-viewer.theseed.org/FIG/index.cgi SEED-Viewer] that allows read-only access to the latest data and annotations. For users interested in editing and learning how to use the system, we also provide a [http://theseed.uchicago.edu/FIG/index.cgi Trial-SEED]. As described in our [[Annotating_1000_genomes|manifesto]] the [[Glossary#annotation|annotation]] is not performed on a gene by gene basis per genome, but rather by [[Glossary#subsystem|Subsystem]] by an expert curator across many genomes at a time. We make all our software and data available for download and use on our [[DownloadPage]] page. * When using the SEED, please cite: Overbeek et al., [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16214803&query_hl=2&itool=pubmed_docsum|Nucleic Acids Res 33(17)], 2005 ([http://www.theseed.org/SubsystemPaperSupplementalMaterial/index.html Supplementary material]) * Our approaches to annotation, gene calling etc are outlined in a series of [[SOPs|Standard Operating Procedures]]. 8e3d490e13d129a91b845e25c6d15d8ba6bde39d 1493 1492 2006-10-27T14:46:32Z FolkerMeyer 2 wikitext text/x-wiki With the growing number of available genomes, the need for an environment to support effective comparative analysis increases. The original SEED Project was started by the [http://thefig.info Fellowship of Interpretation of Genomes (FIG)] as an open source effort. Argonne National Lab and the University of Chicago joined the project, and now much of the activity occurs at those two institutions (as well as the University of Illinois at Urbana-Champaign, Hope college, San Diego State University, the Burnham Institute and a number of other institutions). The cooperative effort focuses on the development of the annotation environment called the SEED and, more importantly, on the development of curated genomic data. We provide a public [http://seed-viewer.theseed.org/FIG/index.cgi SEED-Viewer] that allows read-only access to the latest data and annotations. For users interested in editing and learning how to use the system, we also provide a [http://theseed.uchicago.edu/FIG/index.cgi Trial-SEED]. As described in our [[Annotating_1000_genomes|manifesto]] the [[Glossary#Annotation|annotation]] is not performed on a gene by gene basis per genome, but rather by [[Glossary#Subsystem|subsystem]] by an expert curator across many genomes at a time. We make all our software and data available for download and use on our [[DownloadPage]] page. * When using the SEED, please cite: Overbeek et al., [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16214803&query_hl=2&itool=pubmed_docsum|Nucleic Acids Res 33(17)], 2005 ([http://www.theseed.org/SubsystemPaperSupplementalMaterial/index.html Supplementary material]) * Our approaches to annotation, gene calling etc are outlined in a series of [[SOPs|Standard Operating Procedures]]. da482b15a2bafc1d8cc1582c33e2ec23770a4dbe 1513 1493 2006-11-01T22:27:47Z VeronikaVonstein 6 wikitext text/x-wiki With the growing number of available genomes, the need for an environment to support effective comparative analysis increases. The original SEED Project was started by the [http://thefig.info Fellowship for Interpretation of Genomes (FIG)] as a largely unfunded open source effort in 2003. Argonne National Lab and the University of Chicago joined the project, and now much of the activity occurs at those two institutions (as well as the University of Illinois at Urbana-Champaign, Hope college, San Diego State University, the Burnham Institute and a number of other institutions). The cooperative effort focuses on the development of the comperative genomics environment called the SEED and, more importantly, on the development of curated genomic data. We provide a [http://seed-viewer.theseed.org/FIG/index.cgi SEED-Viewer] that allows read-only access to the latest curated data sets. For users interested in editing and learning how to use the system, we provide the [http://theseed.uchicago.edu/FIG/index.cgi Trial-SEED]. As described in our [[Annotating_1000_genomes|manifesto]] the [[Glossary#Annotation|annotation]] is not performed on a gene by gene basis per genome, but rather by [[Glossary#Subsystem|subsystem]] by an expert curator across many genomes at a time. We make all our software and data available for download and use on our [[DownloadPage]] page. * When using the SEED, please cite: Overbeek et al., [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16214803&query_hl=2&itool=pubmed_docsum|Nucleic Acids Res 33(17)], 2005 ([http://www.theseed.org/SubsystemPaperSupplementalMaterial/index.html Supplementary material]) * Our approaches to annotation, gene calling etc are outlined in a series of [[SOPs|Standard Operating Procedures]]. d33d94aeb255b65cb6b657d7e3c9c900c0870a3b 1514 1513 2006-11-01T22:29:05Z VeronikaVonstein 6 wikitext text/x-wiki With the growing number of available genomes, the need for an environment to support effective comparative analysis increases. The original SEED Project was started in 2003 by the [http://thefig.info Fellowship for Interpretation of Genomes (FIG)] as a largely unfunded open source effort. Argonne National Lab and the University of Chicago joined the project, and now much of the activity occurs at those two institutions (as well as the University of Illinois at Urbana-Champaign, Hope college, San Diego State University, the Burnham Institute and a number of other institutions). The cooperative effort focuses on the development of the comperative genomics environment called the SEED and, more importantly, on the development of curated genomic data. We provide a [http://seed-viewer.theseed.org/FIG/index.cgi SEED-Viewer] that allows read-only access to the latest curated data sets. For users interested in editing and learning how to use the system, we provide the [http://theseed.uchicago.edu/FIG/index.cgi Trial-SEED]. As described in our [[Annotating_1000_genomes|manifesto]] the [[Glossary#Annotation|annotation]] is not performed on a gene by gene basis per genome, but rather by [[Glossary#Subsystem|subsystem]] by an expert curator across many genomes at a time. We make all our software and data available for download and use on our [[DownloadPage]] page. * When using the SEED, please cite: Overbeek et al., [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16214803&query_hl=2&itool=pubmed_docsum|Nucleic Acids Res 33(17)], 2005 ([http://www.theseed.org/SubsystemPaperSupplementalMaterial/index.html Supplementary material]) * Our approaches to annotation, gene calling etc are outlined in a series of [[SOPs|Standard Operating Procedures]]. 896665820009ce5c235c89286d993e37639546fd 0 1367 1483 1460 2006-08-30T16:48:53Z RobEdwards 14 wikitext text/x-wiki === Annotators SEED === The master copy for all data in the SEED environment. Users can not access this password protected site. All annotations are made available via the [[#SEED-Viewer| SEED-Viewer]] and the [[#Trial-SEED|Trial-SEED]]. === Annotation === please see [[#Assigning_a_gene_function_and_annotation| Assigning a gene function and annotation]] === Assigning a gene function and annotation === Annotators assign gene functions to genes, and we call this process annotation. In most contexts, people use the term annotation to refer to assignments of function to the genes within a single organism. We certainly use the term in this sense, but we also use it to describe the process of assigning functions to corresponding genes from numerous genomes. Our basic approach to annotation is to ask our annotators to annotate the genes included in a [[#subsystem|Subsystem]] (e.g., glycolysis) across all genomes. This process of annotation of the genes within a subsystem across a set of genomes, rather than annotation of genes within a single genome, allows our annotators to focus on a constrained set of functional roles and attempt to accurately identify exactly what variant, if any, of a subsystem exists in each of the genomes. We use the term annotation to refer to assigning functions to genes (either within a single organism or to a constrained set of gene/protein families across a set of organisms). This activity certainly is closely related to the construction of subsystems and protein families (which we call FIGfams), but we will describe those activities elsewhere. === Assignment === please see [[#Assigning_a_gene_function_and_annotation| Assigning a gene function and annotation]] === Bidirectional Best Hit === The paper [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=EBI&pubmedid=10077608 The use of gene clusters to infer functional coupling] defines a Bidirectional Best Hit or BBH as follows: <blockquote> Given two genes Xa and Xb from two genomes Ga and Gb, Xa and Xb are called a “bidirectional best hit (BBH)” if and only if recognizable similarity exists between them (in our case, we required fasta3 scores lower than 1.0 × 10−5), there is no gene Zb in Gb that is more similar than Xb is to Xa, and there is no gene Za in Ga that is more similar than Xa is to Xb. Genes (Xa, Ya) from Ga and (Xb, Yb) from Gb form a “pair of close bidirectional best hits (PCBBH)” if and only if Xa and Ya are close, Xb and Yb are close, Xa and Xb are a BBH, and Ya and Yb are a BBH. </blockquote> === Clearinghouse === please see [[#SubsystemClearinghouse|Subsystem Clearinghouse]] === FIGfam === FIGfams are protein families generated by the Fellowship for Interpretation of Genomes (FIG). These families are based on the collection of subsystems, as well as correspondences between genes in closely related strains (we describe the construction of FIGfams in a separate SOP). The important properties of these families are as follows: # Two PEGs which both occur within a single FIGfam are believed to have the same function. # There is a decision procedure associated with the family which can be invoked to determine whether or not a gene can be “safely” assigned the function associated with the family. === Functional role === The concept of functional role is both basic and primitive in the sense that we will not pretend to offer a precise definition. It corresponds roughly to a single logical role that a gene or gene product may play in the operation of a cell. === Gene function === The function of a protein-encoding gene (PEG) is the functional role played by the product of the gene or an expression describing a set of roles played by the encoded protein. The operators used to construct expressions and the meanings associated with the operators are described in http://www.nmpdr.org/FIG/Html/SEED_functions.html Genes other than PEGs can also be assigned functions (e.g., SSU rRNA). However, in most cases the functions assigned to genes other than PEGs tend not to be problematic. === Metabolic Reconstruction === When we use the term metabolic reconstruction of a given genome we will simply mean the set of populated subsystems that contain the genome, the PEGs (and their assigned functions) that are connected to functional roles in these populated subsystems, and the specific variant code associated with the genome in each of the populated subsystems. === NMPDR pathogen genome === The NMPDR is responsible for five classes of genomes: # Campylobacter jejuni # Listeria monocytogenes # Staphylococcus aureus # Streptococcus pneumoniae and Streptococcus pyogenes # Pathogenic Vibrio === PEG === A Protein Encoding Gene (PEG) is equivalent to a CDS (Coding Sequence). === Populated Subsystem === please see [[#Subsystem|Subsystem]] === SEED-Viewer === A read-only version of the SEED that presents the latest data. http://seed-viewer.theseed.org '''Please note''': The data is updated automatically every 24 hours. When citing or linking to the SEED please use this version. === Subsystem === A subsystem is a set of functional roles that an annotator has decided should be thought of as related. Frequently, subsystems represent the collection of [[#Functional_role|functional roles]] that make up a metabolic pathway, a complex (e.g., the ribosome), or a class of proteins (e.g., two-component signal-transduction proteins within Staphylococcus aureus). A '''populated subsystem''' is a subsystem with an attached spreadsheet. The rows of the spreadsheet represent genomes and the columns represent the functional roles of the spreadsheet. Each cell contains the identifiers of genes from the corresponding genome the implement the specific functional role. That is, a populated subsystem specifies which genes implement instances of the subsystem in each of the genomes. The rows of a populated genome are assigned '''variant codes''' which describe which of a set of possible variants of the subsystem exist within each genome (special codes expressing a total absence of the subsystem or remaining uncertainty exist). Construction of a large set of curated populated subsystems is at the center of the NMPDR and SEED annotation efforts. === Subsystem Clearing House === Since annotators can work on any machine (including the public SEED) the way to propagate subsystems is via http://clearinghouse.theseed.org/clearinghouse_browser.cgi? === Trial-SEED === A public, read-write copy of the SEED is made available on http://theseed.uchicago.edu/FIG/index.cgi '''Please note''': The data on this server is updated in irregular intervals. Users should not assume that annotations made on this system will persist. Please publish your annotations to the [[#Subsystem_clearing_house|Subsystem Clearing house]]. === Variant Code=== please see [[#Subsystem|Subsystem]] 1d98cccd6b023b1fd649810c88a87c58d9b4cb88 1484 1483 2006-08-30T17:29:12Z RobEdwards 14 wikitext text/x-wiki === Annotators SEED === The master copy for all data in the SEED environment. Users can not access this password protected site. All annotations are made available via the [[#SEED-Viewer| SEED-Viewer]] and the [[#Trial-SEED|Trial-SEED]]. === Annotation === please see [[#Assigning_a_gene_function_and_annotation| Assigning a gene function and annotation]] === Assigning a gene function and annotation === Annotators assign gene functions to genes, and we call this process annotation. In most contexts, people use the term annotation to refer to assignments of function to the genes within a single organism. We certainly use the term in this sense, but we also use it to describe the process of assigning functions to corresponding genes from numerous genomes. Our basic approach to annotation is to ask our annotators to annotate the genes included in a [[#subsystem|Subsystem]] (e.g., glycolysis) across all genomes. This process of annotation of the genes within a subsystem across a set of genomes, rather than annotation of genes within a single genome, allows our annotators to focus on a constrained set of functional roles and attempt to accurately identify exactly what variant, if any, of a subsystem exists in each of the genomes. We use the term annotation to refer to assigning functions to genes (either within a single organism or to a constrained set of gene/protein families across a set of organisms). This activity certainly is closely related to the construction of subsystems and protein families (which we call FIGfams), but we will describe those activities elsewhere. === Assignment === please see [[#Assigning_a_gene_function_and_annotation| Assigning a gene function and annotation]] === Bidirectional Best Hit (BBH) === The paper [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=EBI&pubmedid=10077608 The use of gene clusters to infer functional coupling] defines a Bidirectional Best Hit or BBH as follows: <blockquote> Given two genes Xa and Xb from two genomes Ga and Gb, Xa and Xb are called a “bidirectional best hit (BBH)” if and only if recognizable similarity exists between them (in our case, we required fasta3 scores lower than 1.0 × 10−5), there is no gene Zb in Gb that is more similar than Xb is to Xa, and there is no gene Za in Ga that is more similar than Xa is to Xb. Genes (Xa, Ya) from Ga and (Xb, Yb) from Gb form a “pair of close bidirectional best hits (PCBBH)” if and only if Xa and Ya are close, Xb and Yb are close, Xa and Xb are a BBH, and Ya and Yb are a BBH. </blockquote> === Clearinghouse === please see [[#SubsystemClearinghouse|Subsystem Clearinghouse]] === FIGfam === FIGfams are protein families generated by the Fellowship for Interpretation of Genomes (FIG). These families are based on the collection of subsystems, as well as correspondences between genes in closely related strains (we describe the construction of FIGfams in a separate SOP). The important properties of these families are as follows: # Two PEGs which both occur within a single FIGfam are believed to have the same function. # There is a decision procedure associated with the family which can be invoked to determine whether or not a gene can be “safely” assigned the function associated with the family. === Functional role === The concept of functional role is both basic and primitive in the sense that we will not pretend to offer a precise definition. It corresponds roughly to a single logical role that a gene or gene product may play in the operation of a cell. === Gene function === The function of a protein-encoding gene (PEG) is the functional role played by the product of the gene or an expression describing a set of roles played by the encoded protein. The operators used to construct expressions and the meanings associated with the operators are described in http://www.nmpdr.org/FIG/Html/SEED_functions.html Genes other than PEGs can also be assigned functions (e.g., SSU rRNA). However, in most cases the functions assigned to genes other than PEGs tend not to be problematic. === Metabolic Reconstruction === When we use the term metabolic reconstruction of a given genome we will simply mean the set of populated subsystems that contain the genome, the PEGs (and their assigned functions) that are connected to functional roles in these populated subsystems, and the specific variant code associated with the genome in each of the populated subsystems. === NMPDR pathogen genome === The NMPDR is responsible for five classes of genomes: # Campylobacter jejuni # Listeria monocytogenes # Staphylococcus aureus # Streptococcus pneumoniae and Streptococcus pyogenes # Pathogenic Vibrio === Pair of Close Homologs (PCH) === The paper [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=EBI&pubmedid=10077608 The use of gene clusters to infer functional coupling] defines a Pair of Close Homologs as follows: <blockquote> We can also define the concept of “pairs of close homologs” (PCHs) as follows: genes (X′a, Y′a) from Ga and (X′b, Y′b) from Gb form a PCH if and only if X′a and Y′a are close, X′b and Y′b are close, X′a and X′b are recognizably similar, and Y′a and Y′b are recognizably similar. Here, we will consider two genes to be recognizably similar if their gene products produce fasta3 scores lower than 1.0 × 10−5. We use a scoring scheme analogous to the one described for PCBBHs to evaluate the connections between PCHs, except that if Ga and Gb are the same genome, we assign an arbitrary “same-genome score” (“same-genome” pairs cannot occur for PCBBHs by definition, but for PCHs they are possible). Unlike PCBBHs from two very close genomes for which contiguity is completely uninformative in the vast majority of cases, PCHs allow recognition of gene clusters that play similar (but usually not identical) roles (such as two transport cassettes containing pairs of homologs) in the same or similar organisms. The arbitrary “same-genome score” should, we believe, have a value that is high enough to rank such instances as significant. </blockquote> === PEG === A Protein Encoding Gene (PEG) is equivalent to a CDS (Coding Sequence). === Populated Subsystem === please see [[#Subsystem|Subsystem]] === SEED-Viewer === A read-only version of the SEED that presents the latest data. http://seed-viewer.theseed.org '''Please note''': The data is updated automatically every 24 hours. When citing or linking to the SEED please use this version. === Subsystem === A subsystem is a set of functional roles that an annotator has decided should be thought of as related. Frequently, subsystems represent the collection of [[#Functional_role|functional roles]] that make up a metabolic pathway, a complex (e.g., the ribosome), or a class of proteins (e.g., two-component signal-transduction proteins within Staphylococcus aureus). A '''populated subsystem''' is a subsystem with an attached spreadsheet. The rows of the spreadsheet represent genomes and the columns represent the functional roles of the spreadsheet. Each cell contains the identifiers of genes from the corresponding genome the implement the specific functional role. That is, a populated subsystem specifies which genes implement instances of the subsystem in each of the genomes. The rows of a populated genome are assigned '''variant codes''' which describe which of a set of possible variants of the subsystem exist within each genome (special codes expressing a total absence of the subsystem or remaining uncertainty exist). Construction of a large set of curated populated subsystems is at the center of the NMPDR and SEED annotation efforts. === Subsystem Clearing House === Since annotators can work on any machine (including the public SEED) the way to propagate subsystems is via http://clearinghouse.theseed.org/clearinghouse_browser.cgi? === Trial-SEED === A public, read-write copy of the SEED is made available on http://theseed.uchicago.edu/FIG/index.cgi '''Please note''': The data on this server is updated in irregular intervals. Users should not assume that annotations made on this system will persist. Please publish your annotations to the [[#Subsystem_clearing_house|Subsystem Clearing house]]. === Variant Code=== please see [[#Subsystem|Subsystem]] bcbf31a44f9956d5705cd717e944976cadfadd2d 1511 1484 2006-11-01T19:06:47Z Mkubal 15 wikitext text/x-wiki === Annotators SEED === The master copy for all data in the SEED environment. Users can not access this password protected site. All annotations are made available via the [[#SEED-Viewer| SEED-Viewer]] and the [[#Trial-SEED|Trial-SEED]]. === Annotation === please see [[#Assigning_a_gene_function_and_annotation| Assigning a gene function and annotation]] === Assigning a gene function and annotation === Annotators assign gene functions to genes, and we call this process annotation. In most contexts, people use the term annotation to refer to assignments of function to the genes within a single organism. We certainly use the term in this sense, but we also use it to describe the process of assigning functions to corresponding genes from numerous genomes. Our basic approach to annotation is to ask our annotators to annotate the genes included in a [[#subsystem|Subsystem]] (e.g., glycolysis) across all genomes. This process of annotation of the genes within a subsystem across a set of genomes, rather than annotation of genes within a single genome, allows our annotators to focus on a constrained set of functional roles and attempt to accurately identify exactly what variant, if any, of a subsystem exists in each of the genomes. We use the term annotation to refer to assigning functions to genes (either within a single organism or to a constrained set of gene/protein families across a set of organisms). This activity certainly is closely related to the construction of subsystems and protein families (which we call FIGfams), but we will describe those activities elsewhere. === Assignment === please see [[#Assigning_a_gene_function_and_annotation| Assigning a gene function and annotation]] === Bidirectional Best Hit (BBH) === The paper [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=EBI&pubmedid=10077608 The use of gene clusters to infer functional coupling] defines a Bidirectional Best Hit or BBH as follows: <blockquote> Given two genes Xa and Xb from two genomes Ga and Gb, Xa and Xb are called a “bidirectional best hit (BBH)” if and only if recognizable similarity exists between them (in our case, we required fasta3 scores lower than 1.0 × 10−5), there is no gene Zb in Gb that is more similar than Xb is to Xa, and there is no gene Za in Ga that is more similar than Xa is to Xb. Genes (Xa, Ya) from Ga and (Xb, Yb) from Gb form a “pair of close bidirectional best hits (PCBBH)” if and only if Xa and Ya are close, Xb and Yb are close, Xa and Xb are a BBH, and Ya and Yb are a BBH. </blockquote> === Clearinghouse === please see [[#SubsystemClearinghouse|Subsystem Clearinghouse]] ===Feature=== A feature is a defined region in the DNA. A PEG is the most prevalent feature type in the SEED. Some other feature types include RNA, prophage and pathogenicity islands. The format for a feature ID is fig|genome_id.feature_abbreviation.feature_number (ie fig|83333.1.peg.100 ). === FIGfam === FIGfams are protein families generated by the Fellowship for Interpretation of Genomes (FIG). These families are based on the collection of subsystems, as well as correspondences between genes in closely related strains (we describe the construction of FIGfams in a separate SOP). The important properties of these families are as follows: # Two PEGs which both occur within a single FIGfam are believed to have the same function. # There is a decision procedure associated with the family which can be invoked to determine whether or not a gene can be “safely” assigned the function associated with the family. === Functional role === The concept of functional role is both basic and primitive in the sense that we will not pretend to offer a precise definition. It corresponds roughly to a single logical role that a gene or gene product may play in the operation of a cell. === Gene function === The function of a protein-encoding gene (PEG) is the functional role played by the product of the gene or an expression describing a set of roles played by the encoded protein. The operators used to construct expressions and the meanings associated with the operators are described in http://www.nmpdr.org/FIG/Html/SEED_functions.html Genes other than PEGs can also be assigned functions (e.g., SSU rRNA). However, in most cases the functions assigned to genes other than PEGs tend not to be problematic. === Metabolic Reconstruction === When we use the term metabolic reconstruction of a given genome we will simply mean the set of populated subsystems that contain the genome, the PEGs (and their assigned functions) that are connected to functional roles in these populated subsystems, and the specific variant code associated with the genome in each of the populated subsystems. === NMPDR pathogen genome === The NMPDR is responsible for five classes of genomes: # Campylobacter jejuni # Listeria monocytogenes # Staphylococcus aureus # Streptococcus pneumoniae and Streptococcus pyogenes # Pathogenic Vibrio === Pair of Close Homologs (PCH) === The paper [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=EBI&pubmedid=10077608 The use of gene clusters to infer functional coupling] defines a Pair of Close Homologs as follows: <blockquote> We can also define the concept of “pairs of close homologs” (PCHs) as follows: genes (X′a, Y′a) from Ga and (X′b, Y′b) from Gb form a PCH if and only if X′a and Y′a are close, X′b and Y′b are close, X′a and X′b are recognizably similar, and Y′a and Y′b are recognizably similar. Here, we will consider two genes to be recognizably similar if their gene products produce fasta3 scores lower than 1.0 × 10−5. We use a scoring scheme analogous to the one described for PCBBHs to evaluate the connections between PCHs, except that if Ga and Gb are the same genome, we assign an arbitrary “same-genome score” (“same-genome” pairs cannot occur for PCBBHs by definition, but for PCHs they are possible). Unlike PCBBHs from two very close genomes for which contiguity is completely uninformative in the vast majority of cases, PCHs allow recognition of gene clusters that play similar (but usually not identical) roles (such as two transport cassettes containing pairs of homologs) in the same or similar organisms. The arbitrary “same-genome score” should, we believe, have a value that is high enough to rank such instances as significant. </blockquote> === PEG === A Protein Encoding Gene (PEG) is equivalent to a CDS (Coding Sequence). === Populated Subsystem === please see [[#Subsystem|Subsystem]] === SEED-Viewer === A read-only version of the SEED that presents the latest data. http://seed-viewer.theseed.org '''Please note''': The data is updated automatically every 24 hours. When citing or linking to the SEED please use this version. === Subsystem === A subsystem is a set of functional roles that an annotator has decided should be thought of as related. Frequently, subsystems represent the collection of [[#Functional_role|functional roles]] that make up a metabolic pathway, a complex (e.g., the ribosome), or a class of proteins (e.g., two-component signal-transduction proteins within Staphylococcus aureus). A '''populated subsystem''' is a subsystem with an attached spreadsheet. The rows of the spreadsheet represent genomes and the columns represent the functional roles of the spreadsheet. Each cell contains the identifiers of genes from the corresponding genome the implement the specific functional role. That is, a populated subsystem specifies which genes implement instances of the subsystem in each of the genomes. The rows of a populated genome are assigned '''variant codes''' which describe which of a set of possible variants of the subsystem exist within each genome (special codes expressing a total absence of the subsystem or remaining uncertainty exist). Construction of a large set of curated populated subsystems is at the center of the NMPDR and SEED annotation efforts. === Subsystem Clearing House === Since annotators can work on any machine (including the public SEED) the way to propagate subsystems is via http://clearinghouse.theseed.org/clearinghouse_browser.cgi? === Trial-SEED === A public, read-write copy of the SEED is made available on http://theseed.uchicago.edu/FIG/index.cgi '''Please note''': The data on this server is updated in irregular intervals. Users should not assume that annotations made on this system will persist. Please publish your annotations to the [[#Subsystem_clearing_house|Subsystem Clearing house]]. === Variant Code=== please see [[#Subsystem|Subsystem]] ea351717c17eec05378707dd832df0b9de2163e3 0 1375 1485 1420 2006-08-30T19:11:24Z FolkerMeyer 2 wikitext text/x-wiki If you want to contact us please use the following email address: [mailto:info@theseed.org] 3210fcbf393f8a760febd80768a0ca8c95301ac4 0 1382 1491 2006-10-13T21:49:31Z DanielPaarmann 8 wikitext text/x-wiki == HOPS Database == ('''H'''ypotheses and '''O'''pen '''P'''roblems revealed by '''S'''ubsystems) Sequencing and analysis of hundreds, soon to be thousands, of genomes reveals multiple gaps in our knowledge of basic biochemical and cellular processes. Accurate mapping of the revealed open problems within a framework of specific subsystems and groups of organisms sets the stage for generating hypotheses amenable to experimental validation. In a growing number of cases, predictions of novel genes and pathways delivered by comparative genomics techniques (eg analysis of gene clustering on prokaryotic chromosomes) get successfully verified. [http://www.theseed.org/HOPSS/HOPSS.cgi HOPS Database] == EGGS database: Essential Genes on Genome Scale == SEED maintains an up-to-date database of all microbial gene essentiality data experimentally obtained in the currently published genome-scale gene essentiality screens (listed in Table 1). Comparative analysis of these data across multiple organisms in a rich genomic, biochemical, and phylogenetic contexts provided by the collection of annotated Subsystems greatly facilitates their interpretation and practical applications, such as, understanding of cellular networks, gene and pathway discovery, identification of novel drug targets, and strain engineering. [http://theseed.uchicago.edu/FIG/eggs.cgi EGGS Database] f136b7abd9c812e4e331467fa03d7fd0484143cb 0 1383 1497 2006-10-31T16:11:40Z FolkerMeyer 2 Initial version of the SEED FAQ wikitext text/x-wiki == '''SEED-FAQ''': A list of Frequently Asked Questions about the SEED annotation framework. == * Is the SEED available? Yes, the SEED is completely open source. Please check our download site. * What genomes are included in the SEED data set? We currently attempt to include all available genomes. * How often is the SEED updated? We attempt to include new genomes as they become available. * What is the difference between SEED and the SEED-Viewer? The SEED is a complex application used for both the curation of [[Glossary#Subsystems|subsystems]] and the [[Glossary#Annotation|annotation]] of sequence data. It is used on a private machine for data curation, a publicly writable [http://theseed.uchicago.edu/FIG/index.cgi copy of the SEED] is available for testing purposes. The [http://seed-viewer.theseed.org/ SEED-Viewer] is the preferred entry point for users interested in our curated data sets of genomes and subsystems. * What data is available inside the SEED-Viewer? The data underlying the SEED-viewer is updated on a nightly basis from the main curation machine. Work in progress is not made available on the SEED-Viewer, except for that the SEED-Viewer is a complete replicate of the main SEED server. * Can I link my web site to the SEED? YES. We provide stable IDs for our genomes and genome features and a mechanisms to construct hyperlinks. The base URL: http://link.theseed.org/linkin.cgi?id= will link to the web page for a specific SEED data object. Example: http://link.theseed.org/linkin.cgi?id=fig|83331.1.peg.2 * What platforms do you run SEED on? Our main platforms are MacOSX (Intel and PPC) and Linux (Intel and PPC), there is no reason the SEED should not run on other platforms, we do however not perform testing etc. * Can I annotate my genome with the SEED? As of now, inclusion of genomes in the SEED can only be done in two ways, install a local instance and work with that or request inclusion of your genome via email. However we are planning to make available a genome annotation service based on SEED technology. * Are there other similar efforts our there? Yes. Currently we are aware of [http://www.tigr.org TIGR's] Comprehensive Microbial Resource ([http://cmr.tigr.org CMR]) and [http://www.jgi.doe.gov JGI's] Integrated Microbial Genomes ([http://img.jgi.doe.gov IMG]). * What is the difference between SEED and other annotation approaches? Annotations in the SEED are built on two main pieces of evidence, sequence similarity and conservation on the chromosome. Most other systems merely rely on sequence similarity. In addition to this, the SEED approach to annotation is based on the concept of having expert annotators curate [[Glossary#Subsystems|subsystems]] of functionally related [[Glossary#Functional role|functional roles]]. 90b68b27373b06a440e940c840243491bc9497f1 1498 1497 2006-10-31T16:12:23Z FolkerMeyer 2 wikitext text/x-wiki == '''SEED-FAQ''': A list of Frequently Asked Questions about the SEED annotation framework. == * Is the SEED available? Yes, the SEED is completely open source. Please check our download site. * What genomes are included in the SEED data set? We currently attempt to include all available genomes. * How often is the SEED updated? We attempt to include new genomes as they become available. * What is the difference between SEED and the SEED-Viewer? The SEED is a complex application used for both the curation of [[Glossary#Subsystems|subsystems]] and the [[Glossary#Annotation|annotation]] of sequence data. It is used on a private machine for data curation, a publicly writable [http://theseed.uchicago.edu/FIG/index.cgi copy of the SEED] is available for testing purposes. The [http://seed-viewer.theseed.org/ SEED-Viewer] is the preferred entry point for users interested in our curated data sets of genomes and subsystems. * What data is available inside the SEED-Viewer? The data underlying the SEED-viewer is updated on a nightly basis from the main curation machine. Work in progress is not made available on the SEED-Viewer, except for that the SEED-Viewer is a complete replicate of the main SEED server. * Can I link my web site to the SEED? YES. We provide stable IDs for our genomes and genome features and a mechanisms to construct hyperlinks. The base URL: http://link.theseed.org/linkin.cgi?id= will link to the web page for a specific SEED data object. Example: http://link.theseed.org/linkin.cgi?id=fig|83331.1.peg.2 * What platforms do you run SEED on? Our main platforms are MacOSX (Intel and PPC) and Linux (Intel and PPC), there is no reason the SEED should not run on other platforms, we do however not perform testing etc. * Can I annotate my genome with the SEED? As of now, inclusion of genomes in the SEED can only be done in two ways, install a local instance and work with that or request inclusion of your genome via email. However we are planning to make available a genome annotation service based on SEED technology. * Are there other similar efforts our there? Yes. Currently we are aware of [http://www.tigr.org TIGR's] Comprehensive Microbial Resource ([http://cmr.tigr.org CMR]) and [http://www.jgi.doe.gov JGI's] Integrated Microbial Genomes ([http://img.jgi.doe.gov IMG]). * What is the difference between SEED and other annotation approaches? Annotations in the SEED are built on two main pieces of evidence, sequence similarity and conservation on the chromosome. Most other systems merely rely on sequence similarity. In addition to this, the SEED approach to annotation is based on the concept of having expert annotators curate [[Glossary#Subsystems|subsystems]] of functionally related [[Glossary#Functional role|functional roles]]. 2ce763c32abc66c4ecc5ef906607711027e737d1 1499 1498 2006-10-31T21:17:09Z FolkerMeyer 2 wikitext text/x-wiki == '''SEED-FAQ''': A list of Frequently Asked Questions about the SEED annotation framework. == * Is the SEED available? Yes, the SEED is completely open source. Both our source code and the accompanying data are available. Please check our [[DownloadPage|download site]]. * What genomes are included in the SEED data set? ''This is a placeholder for a PAGE that has a pointer to our genomelist.'' * How often is the SEED updated? The SEED is continuously updated, as new genomes are becoming available from the sequencing centers and/or NCBI's GenBank. * What is the difference between SEED and the SEED-Viewer? The SEED is a complex application used for both the curation of [[Glossary#Subsystems|subsystems]] and the [[Glossary#Annotation|annotation]] of sequence data. It is used on a private machine for data curation, a publicly writable [http://theseed.uchicago.edu/FIG/index.cgi copy of the SEED] is available for testing purposes. The [http://seed-viewer.theseed.org/ SEED-Viewer] is the preferred entry point for users interested in our curated data sets of genomes and subsystems. * What data is available inside the SEED-Viewer? The data underlying the SEED-viewer is updated on a nightly basis from the main curation machine. Work in progress is not made available on the SEED-Viewer, except for that the SEED-Viewer is a complete replicate of the main SEED server. * Can I link my web site to the SEED? YES. We provide stable IDs for our genomes and genome features and a mechanisms to construct hyperlinks. The base URL: http://link.theseed.org/linkin.cgi?id= will link to the web page for a specific SEED data object. Example: http://link.theseed.org/linkin.cgi?id=fig|83331.1.peg.2 * What platforms do you run SEED on? Our main platforms are MacOSX (Intel and PPC) and Linux (Intel and PPC), there is no reason the SEED should not run on other platforms, we do however not perform testing etc. * Can I annotate my genome with the SEED? As of now, inclusion of genomes in the SEED can only be done in two ways, install a local instance and work with that or request inclusion of your genome via email. However we are planning to make available a genome annotation service based on SEED technology. * Are there other similar efforts our there? Yes. Currently we are aware of [http://www.tigr.org TIGR's] Comprehensive Microbial Resource ([http://cmr.tigr.org CMR]) and [http://www.jgi.doe.gov JGI's] Integrated Microbial Genomes ([http://img.jgi.doe.gov IMG]). * What is the difference between SEED and other annotation approaches? Annotations in the SEED are built on two main pieces of evidence, sequence similarity and conservation on the chromosome. Most other systems merely rely on sequence similarity. In addition to this, the SEED approach to annotation is based on the concept of having expert annotators curate [[Glossary#Subsystems|subsystems]] of functionally related [[Glossary#Functional role|functional roles]]. 0eaa63d873ab7fd1a009eeec5b792e2bd2263209 1500 1499 2006-10-31T21:19:31Z FolkerMeyer 2 /* '''SEED-FAQ''': A list of Frequently Asked Questions about the SEED annotation framework. */ wikitext text/x-wiki == '''SEED-FAQ''': A list of Frequently Asked Questions about the SEED annotation framework. == * Is the SEED available? Yes, the SEED is completely open source. Both our source code and the accompanying data are available. Please check our [[DownloadPage|download site]]. * What genomes are included in the SEED data set? ''This is a placeholder for a PAGE that has a pointer to our genomelist.'' * How often is the SEED updated? The SEED is continuously updated, as new genomes are becoming available from the sequencing centers and/or NCBI's GenBank. * What is the difference between SEED and the SEED-Viewer? The SEED is a complex application used for both the curation of [[Glossary#Subsystems|subsystems]] and the [[Glossary#Annotation|annotation]] of sequence data. It is used on a private machine for data curation, a publicly writable [http://theseed.uchicago.edu/FIG/index.cgi copy of the SEED] is available for testing purposes. The [http://seed-viewer.theseed.org/ SEED-Viewer] is a user-friendly, read-only interface to our curated data sets of genomes and subsystems. * What data is available inside the SEED-Viewer? The data underlying the SEED-viewer is updated on a nightly basis from the main curation machine. Work in progress is not made available on the SEED-Viewer, except for that the SEED-Viewer is a complete replicate of the main SEED server. * Can I link my web site to the SEED? YES. We provide stable IDs for our genomes and genome features and a mechanisms to construct hyperlinks. The base URL: http://link.theseed.org/linkin.cgi?id= will link to the web page for a specific SEED data object. Example: http://link.theseed.org/linkin.cgi?id=fig|83331.1.peg.2 * What platforms do you run SEED on? Our main platforms are MacOSX (Intel and PPC) and Linux (Intel and PPC), there is no reason the SEED should not run on other platforms, we do however not perform testing etc. * Can I annotate my genome with the SEED? As of now, inclusion of genomes in the SEED can only be done in two ways, install a local instance and work with that or request inclusion of your genome via email. However we are planning to make available a genome annotation service based on SEED technology. * Are there other similar efforts our there? Yes. Currently we are aware of [http://www.tigr.org TIGR's] Comprehensive Microbial Resource ([http://cmr.tigr.org CMR]) and [http://www.jgi.doe.gov JGI's] Integrated Microbial Genomes ([http://img.jgi.doe.gov IMG]). * What is the difference between SEED and other annotation approaches? Annotations in the SEED are built on two main pieces of evidence, sequence similarity and conservation on the chromosome. Most other systems merely rely on sequence similarity. In addition to this, the SEED approach to annotation is based on the concept of having expert annotators curate [[Glossary#Subsystems|subsystems]] of functionally related [[Glossary#Functional role|functional roles]]. 85350a221db544452e23693c1a0879667787a3a5 1501 1500 2006-10-31T21:28:41Z FolkerMeyer 2 wikitext text/x-wiki == '''SEED-FAQ''': A list of Frequently Asked Questions about the SEED annotation framework. == * Is the SEED available? Yes, the SEED is completely open source. Both our source code and the accompanying data are available. Please check our [[DownloadPage|download site]]. * What genomes are included in the SEED data set? ''This is a placeholder for a PAGE that has a pointer to our genomelist.'' * How often is the SEED updated? The SEED is continuously updated, as new genomes are becoming available from the sequencing centers and/or NCBI's GenBank. * What is the difference between SEED and the SEED-Viewer? The SEED is a complex application used for both the curation of [[Glossary#Subsystems|subsystems]] and the [[Glossary#Annotation|annotation]] of sequence data. It is used on a private machine for data curation, a publicly writable [http://theseed.uchicago.edu/FIG/index.cgi copy of the SEED] is available for testing purposes. The [http://seed-viewer.theseed.org/ SEED-Viewer] is a user-friendly, read-only interface to our curated data sets of genomes and subsystems. * What data is available inside the SEED-Viewer? All data from the associated SEED database is available for exploration in the SEED-Viewer. The data underlying the SEED-viewer is updated on a nightly basis from the main curation machine. Work in progress is not made available on the SEED-Viewer, except for that the SEED-Viewer is a complete replicate of the main SEED server. * Can I link my web site to the SEED? YES. We provide stable IDs for our genomes and genome features and a mechanisms to construct hyperlinks. The base URL: http://link.theseed.org/linkin.cgi?id= will link to the web page for a specific SEED data object. Example: http://link.theseed.org/linkin.cgi?id=fig|83331.1.peg.2 * What platforms do you run SEED on? Our main platforms are MacOSX (Intel and PPC) and Linux (Intel and PPC), there is no reason the SEED should not run on other platforms, we do however not perform testing etc. * Can I annotate my genome with the SEED? As of now, inclusion of genomes in the SEED can only be done in two ways, install a local instance and work with that or request inclusion of your genome via email. However we are planning to make available a genome annotation service based on SEED technology. * Are there other similar efforts our there? Yes. Currently we are aware of [http://www.tigr.org TIGR's] Comprehensive Microbial Resource ([http://cmr.tigr.org CMR]) and [http://www.jgi.doe.gov JGI's] Integrated Microbial Genomes ([http://img.jgi.doe.gov IMG]). * What is the difference between SEED and other annotation approaches? Annotations in the SEED are built on two main pieces of evidence, sequence similarity and conservation on the chromosome. Most other systems merely rely on sequence similarity. In addition to this, the SEED approach to annotation is based on the concept of having expert annotators curate [[Glossary#Subsystems|subsystems]] of functionally related [[Glossary#Functional role|functional roles]]. dc1664b4abc33a7ceb9a573df3972446cf0993ad 1502 1501 2006-10-31T21:34:44Z FolkerMeyer 2 wikitext text/x-wiki == '''SEED-FAQ''': A list of Frequently Asked Questions about the SEED annotation framework. == * Is the SEED available? Yes, the SEED is completely open source. Both our source code and the accompanying data are available. Please check our [[DownloadPage|download site]]. * What genomes are included in the SEED data set? ''This is a placeholder for a PAGE that has a pointer to our genomelist.'' * How often is the SEED updated? The SEED is continuously updated, as new genomes are becoming available from the sequencing centers and/or NCBI's GenBank. * What is the difference between SEED and the SEED-Viewer? The SEED is a complex application used for both the curation of [[Glossary#Subsystems|subsystems]] and the [[Glossary#Annotation|annotation]] of sequence data. It is used on a private machine for data curation, a publicly writable [http://theseed.uchicago.edu/FIG/index.cgi copy of the SEED] is available for testing purposes. The [http://seed-viewer.theseed.org/ SEED-Viewer] is a user-friendly, read-only interface to our curated data sets of genomes and subsystems. * What data is available inside the SEED-Viewer? All data from the associated SEED database is available for exploration in the SEED-Viewer. The data underlying the SEED-viewer is updated on a nightly basis from the main curation machine. Work in progress is not made available on the SEED-Viewer, except for that the SEED-Viewer is a complete replicate of the main SEED server. * Can I link my web site to the SEED? YES. We provide stable IDs for our genomes and genome features and a mechanisms to construct hyperlinks. The base URL: http://link.theseed.org/linkin.cgi?id= will link to the web page for a specific SEED data object. Example: http://link.theseed.org/linkin.cgi?id=fig|83331.1.peg.2 * On what platforms do you run SEED? Our platforms are MacOSX (Intel and PPC) and Linux (Debian/ReHat/Fedora on Intel and PPC). * Can I annotate my genome with the SEED? As of now, inclusion of genomes in the SEED can only be done in two ways, install a local instance and work with that or request inclusion of your genome via email. However we are planning to make available a genome annotation service based on SEED technology. * Are there other similar efforts our there? Yes. Currently we are aware of [http://www.tigr.org TIGR's] Comprehensive Microbial Resource ([http://cmr.tigr.org CMR]) and [http://www.jgi.doe.gov JGI's] Integrated Microbial Genomes ([http://img.jgi.doe.gov IMG]). * What is the difference between SEED and other annotation approaches? Annotations in the SEED are built on two main pieces of evidence, sequence similarity and conservation on the chromosome. Most other systems merely rely on sequence similarity. In addition to this, the SEED approach to annotation is based on the concept of having expert annotators curate [[Glossary#Subsystems|subsystems]] of functionally related [[Glossary#Functional role|functional roles]]. d01599a7ea57ba773d4398b2540ee7f6027a400f 1503 1502 2006-10-31T21:36:22Z FolkerMeyer 2 wikitext text/x-wiki == '''SEED-FAQ''': A list of Frequently Asked Questions about the SEED annotation framework. == * Is the SEED available? Yes, the SEED is completely open source. Both our source code and the accompanying data are available. Please check our [[DownloadPage|download site]]. * What genomes are included in the SEED data set? ''This is a placeholder for a PAGE that has a pointer to our genomelist.'' * How often is the SEED updated? The SEED is continuously updated, as new genomes are becoming available from the sequencing centers and/or NCBI's GenBank. * What is the difference between SEED and the SEED-Viewer? The SEED is a complex application used for both the curation of [[Glossary#Subsystems|subsystems]] and the [[Glossary#Annotation|annotation]] of sequence data. It is used on a private machine for data curation, a publicly writable [http://theseed.uchicago.edu/FIG/index.cgi copy of the SEED] is available for testing purposes. The [http://seed-viewer.theseed.org/ SEED-Viewer] is a user-friendly, read-only interface to our curated data sets of genomes and subsystems. * What data is available inside the SEED-Viewer? All data from the associated SEED database is available for exploration in the SEED-Viewer. The data underlying the SEED-viewer is updated on a nightly basis from the main curation machine. Work in progress is not made available on the SEED-Viewer, except for that the SEED-Viewer is a complete replicate of the main SEED server. * Can I link my web site to the SEED? YES. We provide stable IDs for our genomes and genome features and a mechanisms to construct hyperlinks. The base URL: http://link.theseed.org/linkin.cgi?id= will link to the web page for a specific SEED data object. Example: http://link.theseed.org/linkin.cgi?id=fig|83331.1.peg.2 * On what platforms do you run SEED? Our platforms are MacOSX (Intel and PPC) and Linux (Debian/RedHat/Fedora on Intel and PPC). * Can I annotate my genome with the SEED? Yes, however only if your genome is included in the SEED. As of now, inclusion of genomes in the SEED can only be done in two ways, install a local instance and work with that or request inclusion of your genome via email. However we are planning to make available a genome annotation service based on SEED technology. * Are there other similar efforts our there? Yes. Currently we are aware of [http://www.tigr.org TIGR's] Comprehensive Microbial Resource ([http://cmr.tigr.org CMR]) and [http://www.jgi.doe.gov JGI's] Integrated Microbial Genomes ([http://img.jgi.doe.gov IMG]). * What is the difference between SEED and other annotation approaches? Annotations in the SEED are built on two main pieces of evidence, sequence similarity and conservation on the chromosome. Most other systems merely rely on sequence similarity. In addition to this, the SEED approach to annotation is based on the concept of having expert annotators curate [[Glossary#Subsystems|subsystems]] of functionally related [[Glossary#Functional role|functional roles]]. 61c2f0fcd5031265a1410c51c26d6f08e19617b6 1504 1503 2006-10-31T21:37:44Z FolkerMeyer 2 wikitext text/x-wiki == '''SEED-FAQ''': A list of Frequently Asked Questions about the SEED annotation framework. == * Is the SEED available? Yes, the SEED is completely open source. Both our source code and the accompanying data are available. Please check our [[DownloadPage|download site]]. * What genomes are included in the SEED data set? ''This is a placeholder for a PAGE that has a pointer to our genomelist.'' * How often is the SEED updated? The SEED is continuously updated, as new genomes are becoming available from the sequencing centers and/or NCBI's GenBank. * What is the difference between SEED and the SEED-Viewer? The SEED is a complex application used for both the curation of [[Glossary#Subsystems|subsystems]] and the [[Glossary#Annotation|annotation]] of sequence data. It is used on a private machine for data curation, a publicly writable [http://theseed.uchicago.edu/FIG/index.cgi copy of the SEED] is available for testing purposes. The [http://seed-viewer.theseed.org/ SEED-Viewer] is a user-friendly, read-only interface to our curated data sets of genomes and subsystems. * What data is available inside the SEED-Viewer? All data from the associated SEED database is available for exploration in the SEED-Viewer. The data underlying the SEED-viewer is updated on a nightly basis from the main curation machine. Work in progress is not made available on the SEED-Viewer, except for that the SEED-Viewer is a complete replicate of the main SEED server. * Can I link my web site to the SEED? YES. We provide stable IDs for our genomes and genome features and a mechanisms to construct hyperlinks. The base URL: http://link.theseed.org/linkin.cgi?id= will link to the web page for a specific SEED data object. Example: http://link.theseed.org/linkin.cgi?id=fig|83331.1.peg.2 * On what platforms do you run SEED? Our platforms are MacOSX (Intel and PPC) and Linux (Debian/RedHat/Fedora on Intel and PPC). * Can I annotate my genome with the SEED? Yes, but only if your genome is included in the SEED. As of now, inclusion of genomes in the SEED can only be done in two ways, install a local instance and work with that or request inclusion of your genome via email. However we are planning to make available a genome annotation service based on SEED technology. * Are there other similar efforts our there? Yes. Currently we are aware of [http://www.tigr.org TIGR's] Comprehensive Microbial Resource ([http://cmr.tigr.org CMR]) and [http://www.jgi.doe.gov JGI's] Integrated Microbial Genomes ([http://img.jgi.doe.gov IMG]). * What is the difference between SEED and other annotation approaches? Annotations in the SEED are built on two main pieces of evidence, sequence similarity and conservation on the chromosome. Most other systems merely rely on sequence similarity. In addition to this, the SEED approach to annotation is based on the concept of having expert annotators curate [[Glossary#Subsystems|subsystems]] of functionally related [[Glossary#Functional role|functional roles]]. 48e453e16ae720ce06e03a02038e3782cd55b13e 1505 1504 2006-10-31T22:05:36Z FolkerMeyer 2 wikitext text/x-wiki == '''SEED-FAQ''': A list of Frequently Asked Questions about the SEED annotation framework. == * Is the SEED available? Yes, the SEED is completely open source. Both our source code and the accompanying data are available. Please check our [[DownloadPage|download site]]. * What genomes are included in the SEED data set? ''This is a placeholder for a PAGE that has a pointer to our genomelist.'' * How often is the SEED updated? The SEED is continuously updated, as new genomes are becoming available from the sequencing centers and/or NCBI's GenBank. * What is the difference between SEED and the SEED-Viewer? The SEED is a complex application used for both the curation of [[Glossary#Subsystems|subsystems]] and the [[Glossary#Annotation|annotation]] of sequence data. It is used on a private machine for data curation, a publicly writable [http://theseed.uchicago.edu/FIG/index.cgi copy of the SEED] is available for testing purposes. The [http://seed-viewer.theseed.org/ SEED-Viewer] is a user-friendly, read-only interface to our curated data sets of genomes and subsystems. * What is the difference between the SEED, the SEED-Viewer and the metagenomics SEED. While the SEED is the curation platform for genomes, the SEED-Viewer is an application for viewing the data contained. The metagenomics SEED is a special purpose SEED installation for metagenomes. * What data is available inside the SEED-Viewer? All data from the associated SEED database is available for exploration in the SEED-Viewer. The data underlying the SEED-viewer is updated on a nightly basis from the main curation machine. Work in progress is not made available on the SEED-Viewer, except for that the SEED-Viewer is a complete replicate of the main SEED server. * Can I link my web site to the SEED? YES. We provide stable IDs for our genomes and genome features and a mechanisms to construct hyperlinks. The base URL: http://link.theseed.org/linkin.cgi?id= will link to the web page for a specific SEED data object. Example: http://link.theseed.org/linkin.cgi?id=fig|83331.1.peg.2 * On what platforms do you run SEED? Our platforms are MacOSX (Intel and PPC) and Linux (Debian/RedHat/Fedora on Intel and PPC). * Can I annotate my genome with the SEED? Yes, but only if your genome is included in the SEED. As of now, inclusion of genomes in the SEED can only be done in two ways, install a local instance and work with that or request inclusion of your genome via email. However we are planning to make available a genome annotation service based on SEED technology. * Are there other similar efforts our there? Yes. Currently we are aware of [http://www.tigr.org TIGR's] Comprehensive Microbial Resource ([http://cmr.tigr.org CMR]) and [http://www.jgi.doe.gov JGI's] Integrated Microbial Genomes ([http://img.jgi.doe.gov IMG]). * What is the difference between SEED and other annotation approaches? Annotations in the SEED are built on two main pieces of evidence, sequence similarity and conservation on the chromosome. Most other systems merely rely on sequence similarity. In addition to this, the SEED approach to annotation is based on the concept of having expert annotators curate [[Glossary#Subsystems|subsystems]] of functionally related [[Glossary#Functional role|functional roles]]. 04bb18a69e9ea6b6f5aab07d1a3801330f620958 1506 1505 2006-11-01T00:49:20Z VeronikaVonstein 6 wikitext text/x-wiki == '''SEED-FAQ''': A list of Frequently Asked Questions about the SEED comparative environment. == * Is the SEED available? Yes, the SEED is open source. Both our source code and the accompanying data are available. Please check our [[DownloadPage|download site]]. * What genomes are included in the SEED data set? ''This is a placeholder for a PAGE that has a pointer to our genomelist.'' * How often is the SEED updated? The SEED is continuously updated, as new genomes are becoming available from the sequencing centers and/or NCBI's GenBank. * What is the difference between SEED, SEED-Viewer and Trail-SEED? The SEED is a complex environment that is used for the comperative analysis of hudreds of genomes. It allows the annotation [[Glossary#Annotation|annotation]] of sequence data, the integration and visualization of whole-genome data sets (e.g. metabolic reconstructions, microarrya data, essentiality data etc.) and most notably the creation of new and curation of existing [[Glossary#Subsystems|subsystems]]. Our experienced curators and collaborators are using a master instance of the SEED. The [http://seed-viewer.theseed.org/ SEED-Viewer] is a user-friendly, browse-only interface to those curated genomic data sets. The Trail-SEED, a publicly writable [http://theseed.uchicago.edu/FIG/index.cgi] copy of the SEED is available for testing purposes. * What is the difference between the SEED, the SEED-Viewer and the metagenomics SEED. While the SEED is the curation platform for genomes, the SEED-Viewer is an application for viewing the data contained. The metagenomics SEED is a special purpose SEED installation for metagenomes. * What data is available inside the SEED-Viewer? All data from the associated SEED database is available for exploration in the SEED-Viewer. The data underlying the SEED-viewer is updated on a nightly basis from the main curation machine. Work in progress is not made available on the SEED-Viewer, except for that the SEED-Viewer is a complete replicate of the main SEED server. * Can I link my web site to the SEED? YES. We provide stable IDs for our genomes and genome features and a mechanism to construct hyperlinks. The base URL: http://link.theseed.org/linkin.cgi?id= will link to the web page for a specific SEED data object. Example: http://link.theseed.org/linkin.cgi?id=fig|83331.1.peg.2 * On what platforms do you run SEED? Our platforms are MacOSX (Intel and PPC) and Linux (Debian/RedHat/Fedora on Intel and PPC). * Can I annotate my genome with the SEED? Yes, but only if your genome is included in the SEED. As of now, inclusion of genomes in the SEED can only be done in two ways, install a local instance and work with that or request inclusion of your genome via email. However we are planning to make available a genome annotation service based on SEED technology. * Are there other similar efforts out there? Yes. Currently we are aware of [http://www.tigr.org TIGR's] Comprehensive Microbial Resource ([http://cmr.tigr.org CMR]) and [http://www.jgi.doe.gov JGI's] Integrated Microbial Genomes ([http://img.jgi.doe.gov IMG]). * What is the difference between SEED and other annotation approaches? Annotations in the SEED are built on two main pieces of evidence, sequence similarity and conservation on the chromosome. Most other systems merely rely on sequence similarity. In addition to this, the SEED approach to annotation is based on the concept of having expert annotators curate [[Glossary#Subsystems|subsystems]] of functionally related [[Glossary#Functional role|functional roles]]. 418504b5088ec3aee7ad6c4b7f39d3bd4c52daad 1507 1506 2006-11-01T00:50:02Z VeronikaVonstein 6 wikitext text/x-wiki == '''SEED-FAQ''': A list of Frequently Asked Questions about the SEED comparative environment. == * Is the SEED available? Yes, the SEED is open source. Both our source code and the accompanying data are available. Please check our [[DownloadPage|download site]]. * What genomes are included in the SEED data set? ''This is a placeholder for a PAGE that has a pointer to our genomelist.'' * How often is the SEED updated? The SEED is continuously updated, as new genomes are becoming available from the sequencing centers and/or NCBI's GenBank. * What is the difference between SEED, SEED-Viewer and Trail-SEED? The SEED is a complex environment that is used for the comperative analysis of hudreds of genomes. It allows the [[Glossary#Annotation|annotation]] of sequence data, the integration and visualization of whole-genome data sets (e.g. metabolic reconstructions, microarrya data, essentiality data etc.) and most notably the creation of new and curation of existing [[Glossary#Subsystems|subsystems]]. Our experienced curators and collaborators are using a master instance of the SEED. The [http://seed-viewer.theseed.org/ SEED-Viewer] is a user-friendly, browse-only interface to those curated genomic data sets. The Trail-SEED, a publicly writable [http://theseed.uchicago.edu/FIG/index.cgi] copy of the SEED is available for testing purposes. * What is the difference between the SEED, the SEED-Viewer and the metagenomics SEED. While the SEED is the curation platform for genomes, the SEED-Viewer is an application for viewing the data contained. The metagenomics SEED is a special purpose SEED installation for metagenomes. * What data is available inside the SEED-Viewer? All data from the associated SEED database is available for exploration in the SEED-Viewer. The data underlying the SEED-viewer is updated on a nightly basis from the main curation machine. Work in progress is not made available on the SEED-Viewer, except for that the SEED-Viewer is a complete replicate of the main SEED server. * Can I link my web site to the SEED? YES. We provide stable IDs for our genomes and genome features and a mechanism to construct hyperlinks. The base URL: http://link.theseed.org/linkin.cgi?id= will link to the web page for a specific SEED data object. Example: http://link.theseed.org/linkin.cgi?id=fig|83331.1.peg.2 * On what platforms do you run SEED? Our platforms are MacOSX (Intel and PPC) and Linux (Debian/RedHat/Fedora on Intel and PPC). * Can I annotate my genome with the SEED? Yes, but only if your genome is included in the SEED. As of now, inclusion of genomes in the SEED can only be done in two ways, install a local instance and work with that or request inclusion of your genome via email. However we are planning to make available a genome annotation service based on SEED technology. * Are there other similar efforts out there? Yes. Currently we are aware of [http://www.tigr.org TIGR's] Comprehensive Microbial Resource ([http://cmr.tigr.org CMR]) and [http://www.jgi.doe.gov JGI's] Integrated Microbial Genomes ([http://img.jgi.doe.gov IMG]). * What is the difference between SEED and other annotation approaches? Annotations in the SEED are built on two main pieces of evidence, sequence similarity and conservation on the chromosome. Most other systems merely rely on sequence similarity. In addition to this, the SEED approach to annotation is based on the concept of having expert annotators curate [[Glossary#Subsystems|subsystems]] of functionally related [[Glossary#Functional role|functional roles]]. 503ecaf40a26334f7727547cf25f51cc8e85d4ff 1508 1507 2006-11-01T00:52:52Z VeronikaVonstein 6 wikitext text/x-wiki == '''SEED-FAQ''': A list of Frequently Asked Questions about the SEED comparative environment. == * Is the SEED available? Yes, the SEED is open source. Both our source code and the accompanying data are available. Please check our [[DownloadPage|download site]]. * What genomes are included in the SEED data set? ''This is a placeholder for a PAGE that has a pointer to our genomelist.'' * How often is the SEED updated? The SEED is continuously updated, as new genomes are becoming available from the sequencing centers and/or NCBI's GenBank. * What is the difference between SEED, SEED-Viewer and Trail-SEED? The SEED is a complex environment that is used for the comperative analysis of hudreds of genomes. It allows the [[Glossary#Annotation|annotation]] of sequence data, the integration and visualization of whole-genome data sets (e.g. metabolic reconstructions, microarrya data, essentiality data etc.) and most notably the creation of new and curation of existing [[Glossary#Subsystems|subsystems]]. Our experienced curators and collaborators are using a master instance of the SEED. The [http://seed-viewer.theseed.org/ SEED-Viewer] is a user-friendly, browse-only interface to those curated genomic data sets. The [http://theseed.uchicago.edu/FIG/index.cgi/ Trail-SEED], a publicly writable copy of the SEED is available for testing purposes. * What is the difference between the SEED, the SEED-Viewer and the metagenomics SEED. While the SEED is the curation platform for genomes, the SEED-Viewer is an application for viewing the data contained. The metagenomics SEED is a special purpose SEED installation for metagenomes. * What data is available inside the SEED-Viewer? All data from the associated SEED database is available for exploration in the SEED-Viewer. The data underlying the SEED-viewer is updated on a nightly basis from the main curation machine. Work in progress is not made available on the SEED-Viewer, except for that the SEED-Viewer is a complete replicate of the main SEED server. * Can I link my web site to the SEED? YES. We provide stable IDs for our genomes and genome features and a mechanism to construct hyperlinks. The base URL: http://link.theseed.org/linkin.cgi?id= will link to the web page for a specific SEED data object. Example: http://link.theseed.org/linkin.cgi?id=fig|83331.1.peg.2 * On what platforms do you run SEED? Our platforms are MacOSX (Intel and PPC) and Linux (Debian/RedHat/Fedora on Intel and PPC). * Can I annotate my genome with the SEED? Yes, but only if your genome is included in the SEED. As of now, inclusion of genomes in the SEED can only be done in two ways, install a local instance and work with that or request inclusion of your genome via email. However we are planning to make available a genome annotation service based on SEED technology. * Are there other similar efforts out there? Yes. Currently we are aware of [http://www.tigr.org TIGR's] Comprehensive Microbial Resource ([http://cmr.tigr.org CMR]) and [http://www.jgi.doe.gov JGI's] Integrated Microbial Genomes ([http://img.jgi.doe.gov IMG]). * What is the difference between SEED and other annotation approaches? Annotations in the SEED are built on two main pieces of evidence, sequence similarity and conservation on the chromosome. Most other systems merely rely on sequence similarity. In addition to this, the SEED approach to annotation is based on the concept of having expert annotators curate [[Glossary#Subsystems|subsystems]] of functionally related [[Glossary#Functional role|functional roles]]. 016d95771a1e478421cf100a57b368e0aa9440bf 1509 1508 2006-11-01T15:19:26Z FolkerMeyer 2 wikitext text/x-wiki == '''SEED-FAQ''': A list of Frequently Asked Questions about the SEED comparative environment. == * Are the annotations in the SEED computer generated? The [[Glossary#Subsystems|subsystems]] based annotations in the SEED are created by a human expert, in contrast to many existing annotation approaches, the SEED annotation approach is to annotated a [[Glossary#Subsystems|subsystems]] across many genomes at a time by an expert curator. Genes not in subsystems are annotated using an automatic decision procedure. * Is the SEED available? Yes, the SEED is open source. Both our source code and the accompanying data are available. Please check our [[DownloadPage|download site]]. * What genomes are included in the SEED data set? ''This is a placeholder for a PAGE that has a pointer to our genomelist.'' * How often is the SEED updated? The SEED is continuously updated, as new genomes are becoming available from the sequencing centers and/or NCBI's GenBank. * What is the difference between SEED, SEED-Viewer and Trail-SEED? The SEED is a complex environment that is used for the comperative analysis of hudreds of genomes. It allows the [[Glossary#Annotation|annotation]] of sequence data, the integration and visualization of whole-genome data sets (e.g. metabolic reconstructions, microarrya data, essentiality data etc.) and most notably the creation of new and curation of existing [[Glossary#Subsystems|subsystems]]. Our experienced curators and collaborators are using a master instance of the SEED. The [http://seed-viewer.theseed.org/ SEED-Viewer] is a user-friendly, browse-only interface to those curated genomic data sets. The [http://theseed.uchicago.edu/FIG/index.cgi/ Trail-SEED], a publicly writable copy of the SEED is available for testing purposes. * What is the difference between the SEED, the SEED-Viewer and the metagenomics SEED. While the SEED is the curation platform for genomes, the SEED-Viewer is an application for viewing the data contained. The metagenomics SEED is a special purpose SEED installation for metagenomes. * What data is available inside the SEED-Viewer? All data from the associated SEED database is available for exploration in the SEED-Viewer. The data underlying the SEED-viewer is updated on a nightly basis from the main curation machine. Work in progress is not made available on the SEED-Viewer, except for that the SEED-Viewer is a complete replicate of the main SEED server. * Can I link my web site to the SEED? YES. We provide stable IDs for our genomes and genome features and a mechanism to construct hyperlinks. The base URL: http://link.theseed.org/linkin.cgi?id= will link to the web page for a specific SEED data object. Example: http://link.theseed.org/linkin.cgi?id=fig|83331.1.peg.2 * On what platforms do you run SEED? Our platforms are MacOSX (Intel and PPC) and Linux (Debian/RedHat/Fedora on Intel and PPC). * Can I annotate my genome with the SEED? Yes, but only if your genome is included in the SEED. As of now, inclusion of genomes in the SEED can only be done in two ways, install a local instance and work with that or request inclusion of your genome via email. However we are planning to make available a genome annotation service based on SEED technology. * Are there other similar efforts out there? Yes. Currently we are aware of [http://www.tigr.org TIGR's] Comprehensive Microbial Resource ([http://cmr.tigr.org CMR]) and [http://www.jgi.doe.gov JGI's] Integrated Microbial Genomes ([http://img.jgi.doe.gov IMG]). * What is the difference between SEED and other annotation approaches? Annotations in the SEED are built on two main pieces of evidence, sequence similarity and conservation on the chromosome. Most other systems merely rely on sequence similarity. In addition to this, the SEED approach to annotation is based on the concept of having expert annotators curate [[Glossary#Subsystems|subsystems]] of functionally related [[Glossary#Functional role|functional roles]]. 15a952b64d29c1e91ccca459968b9c33c546becf 1510 1509 2006-11-01T15:20:13Z FolkerMeyer 2 wikitext text/x-wiki == '''SEED-FAQ''': A list of Frequently Asked Questions about the SEED comparative environment. == * Are the annotations in the SEED computer generated? The [[Glossary#Subsystems|subsystems]] based annotations in the SEED are created by a human expert, in contrast to many existing annotation approaches, the SEED annotation approach is to annotated a [[Glossary#Subsystems|subsystems]] across many genomes at a time by an expert curator. Genes not in subsystems are annotated using an automatic decision procedure. * Is the SEED available? Yes, the SEED is open source. Both our source code and the accompanying data are available. Please check our [[DownloadPage|download site]]. * What genomes are included in the SEED data set? ''This is a placeholder for a PAGE that has a pointer to our genomelist.'' * How often is the SEED updated? The SEED is continuously updated, as new genomes are becoming available from the sequencing centers and/or NCBI's GenBank. * What is the difference between SEED, SEED-Viewer and Trail-SEED? The SEED is a complex environment that is used for the comperative analysis of hudreds of genomes. It allows the [[Glossary#Annotation|annotation]] of sequence data, the integration and visualization of whole-genome data sets (e.g. metabolic reconstructions, microarrya data, essentiality data etc.) and most notably the creation of new and curation of existing [[Glossary#Subsystems|subsystems]]. Our experienced curators and collaborators are using a master instance of the SEED. The [http://seed-viewer.theseed.org/ SEED-Viewer] is a user-friendly, browse-only interface to those curated genomic data sets. The [http://theseed.uchicago.edu/FIG/index.cgi/ Trail-SEED], a publicly writable copy of the SEED is available for testing purposes. * What is the difference between the SEED, the SEED-Viewer and the metagenomics SEED. While the SEED is the curation platform for genomes, the SEED-Viewer is an application for viewing the data contained. The metagenomics SEED is a special purpose SEED installation for metagenomes. * What data is available inside the SEED-Viewer? All data from the associated SEED database is available for exploration in the SEED-Viewer. The data underlying the SEED-viewer is updated on a nightly basis from the main curation machine. Work in progress is not made available on the SEED-Viewer, except for that the SEED-Viewer is a complete replicate of the main SEED server. * Can I link my web site to the SEED? YES. We provide stable IDs for our genomes and genome features and a mechanism to construct hyperlinks. The base URL: http://link.theseed.org/linkin.cgi?id= will link to the web page for a specific SEED data object. Example: http://link.theseed.org/linkin.cgi?id=fig|83331.1.peg.2 * On what platforms do you run SEED? Our platforms are MacOSX (Intel and PPC) and Linux (Debian/RedHat/Fedora on Intel and PPC). * Can I annotate my genome with the SEED? Yes, but only if your genome is included in the SEED. As of now, inclusion of genomes in the SEED can only be done in two ways, install a local instance and work with that or request inclusion of your genome via email. However we are planning to make available a genome annotation service based on SEED technology. * Are there other similar efforts out there? Yes. Currently we are aware of [http://www.tigr.org TIGR's] Comprehensive Microbial Resource ([http://cmr.tigr.org CMR]) and [http://www.jgi.doe.gov JGI's] Integrated Microbial Genomes ([http://img.jgi.doe.gov IMG]). * What is the difference between SEED and other annotation approaches? Annotations in the SEED are built on two main pieces of evidence, sequence similarity and conservation on the chromosome. Most other systems merely rely on sequence similarity. In addition to this, the SEED approach to annotation is based on the concept of having expert annotators curate [[Glossary#Subsystems|subsystems]] of functionally related [[Glossary#Functional role|functional roles]]. 3f1d801c300bf35ee13cc2d50ea31c6a94ff8773 0 1369 1515 1381 2006-11-01T22:36:07Z VeronikaVonstein 6 wikitext text/x-wiki The Project to Annotate the First 1000 Sequenced Genomes, Develop Detailed Metabolic Reconstructions, and Construct the Corresponding Stoichiometric Matrices by Ross Overbeek === Introduction === In December, 2003 The Fellowship for Interpretation of Genomes (FIG) initiated The Project to Annotate 1000 Genomes (P1K). The explicit goal was to develop a technology for more accurate, high-volume annotation of genomes and to use this technology to provide superior annotations for the first 1000 sequenced genomes. Members of FIG were convinced that the current approaches for high-throughput annotation, based on protein families and automated pipelines that processed genomes sequentially, would ultimately fail to produce annotations of the desired accuracy. We believe that the key to development of high-throughput annotation technology is to have experts annotate single subsystems over the complete collection of genomes. The existing annotation approaches, in which teams analyze a whole genome at a time, ensure that annotators have no special expertise relating to the vast majority of genes they annotate. By having individuals annotate single subsystems over a large collection of genomes, we allow individuals with expertise in specific pathways (or, more generally, subsystems) to perform their task with relatively high accuracy. The early stages of the effort began at FIG, but quickly spread to a number of cooperating institutions, most notably Argonne National Lab. During the first year of the project, we have developed detailed encodings of subsystems that include a majority of the genes from subsystems that make up the core cellular machinery. More importantly, we have developed the initial versions of technology needed to support the project. The Project to Annotate 1000 Genomes has reached the stage where it is clear that it will very shortly produce what we call informal metabolic reconstructions that cover the majority of central metabolism as it is implemented in the close to 300 more-or-less complete genomes that are now available. We think of an informal metabolic reconstruction as a partitioning of the cellular machinery into subsystems, the specification of the functional roles that make up each subsystem, and the inventory of which genes in a specific organism implement the functional roles. What is needed to support both qualitative analysis and effective quantitative modeling is to convert these informal metabolic reconstructions into formal metabolic reconstructions. By a formal reconstruction, we mean an accurate encoding of the metabolic network. The goal of such an encoding is to construct a list of metabolites and a detailed reaction network that is internally consistent (in the sense that metabolites that are produced by reactions are connected as substrates to other reactions or to specific transporters, and that all metabolites that act as substrates are produced by other reactions or provided by transporters). Perhaps, a better way to put this is that all apparent anomalies are highlighted as such, and the essential components of the metabolic network are accurately encoded. The output of such an effort is normally what is termed a stoichiometric matrix, the basic resource required to support stoichiometric modeling. One of the central goals of this enlarged effort is to develop accurate stoichiometric matrices for each of the 1000 genomes; we refer to this component of the effort as The Project to Produce 1000 Stoichiometric Matrices. It is our belief that the development of the technology required to mass-produce accurate genome annotations will ultimately allow fully automated annotation pipelines to achieve relatively high accuracy. Similarly, the existence of 1000 accurate formal metabolic reconstructions would constitute a resource that would allow rapid and accurate development of stoichiometric matrices for newly-sequenced genomes. That is, besides producing accurate annotations, informal metabolic reconstructions, formal metabolic reconstructions, and stoichiometric matrices for a large collection of diverse genomes, we believe that the expanded project will produce technology that will support nearly automatic, very rapid characterization of new genomes. All of the encoded subsystems, metabolic reconstructions and stoichiometric matrices will be made freely available on open web sites. In addition, the software environments used to develop the encoded subsystems and stoichiometric matrices will be developed and supported as open source software. By making the fundamental data items, the encoded subsystems and stoichiometric matrices, freely available to the community, we expect to stimulate development of alternative software systems to support curation and maintenance of these items. === The Project to Annotate 1000 Genomes === We have chosen to conceptually break the Project to Annotate 1000 Genomes into three stages. We discuss these stages as if they will occur sequentially; in fact, all three stages are now in progress. To understand the three stages, the reader must have at least a rudimentary grasp of what we mean by an encoded subsystem and an informal metabolic reconstruction. When we speak of a subsystem, we think of a set of related functional roles. In a specific organism, a set of genes implement these roles, and we think of those genes as constituting the subsystem in that organism. That is, we are really dealing with an abstract notion of subsystem (in which the subsystem is a set of functional roles) and instances of the subsystem in a specific organism (in which a set of genes implements the abstract functional roles). Precisely the same subsystem and functional roles exist in distinct organisms, although obviously the genes are unique to each organism. Subsystems are thought of as possibly having multiple variants. Organisms that have operational versions of a subsystem may well have genes that implement slightly different subsets of the functional roles that make up the subsystem. Each subset of functional roles that exists in at least one organism with an operational version of the subsystem constitutes an operational variant. We think of an informal metabolic reconstruction for an organism as a set of operational variants of subsystems that are believed to exist for the organism. In this conceptualization, one does not have a meaningful functional hierarchy or DAG; rather, we simply have an inventory of functional roles that are implemented in the organism, along with the variants of subsystems that they implement. We do believe that the task of imposing an actual hierarchy is relatively straightforward in comparison with the effort required to construct the set of operational variants. In some contexts, we have included a functional overview in which the subsystems are embedded at the lowest levels. It is clear that, given a diverse collection of informal metabolic reconstructions, the development of appropriate functional hierarchies can be generated with relatively few resources. Our encoding of a subsystem can now be reduced to a specification of a set of functional roles (this amounts to the abstract subsystem) and sets of genes which implement the operational variants in a number of genomes. These genes are given as a subsystem spreadsheet in which each row corresponds to a single genome, each column corresponds to a single functional role, and each cell contains the set of genes in that genome that are believed to implement the given functional role. The Project to Annotate 1000 Genomes amounts to an effort to produce detailed and comprehensive encodings of several hundred subsystems, which will impose assigned functions on genes in each of the genomes. The total percent of genes that can be assigned functions this way is probably on the order of 50-70% in most genomes (in large eukaryotic genomes the total is obviously substantially lower). The percent will grow as our understanding grows. What should be noted is that the accuracy of these assignments will be substantially better than that of current assignments, and the conserved cellular machinery almost all falls within the projected subsystems. Once we have produced our initial set of annotations, we believe that automated pipelines and protein families are excellent tools for propagating them. Protein families are, in fact, a key component of annotation and provide the fundamental mechanism for projection of function between genes. The added dimension provided by subsystems, along with the manual curation required to develop accurate initial encodings of subsystems, is an essential technology for increasing the accuracy and effectiveness of protein families. Ultimately the encoded subsystems will be used to make incremental, essential corrections to collections of protein families (like those supported by UniProt and COGs), and a basis for much more accurate annotation will emerge. === We now proceed to describe the details of the three stages. === ==== Stage 1: Development of Initial Encodings of Subsystems ==== The initial stage of the project will involve development of approximately 100-150 subsystems that will cover most of the conserved cellular machinery in prokaryotes (and all of the central metabolic machinery in eukaryotes). This work will be done largely by trained annotators who achieve a limited mastery of specific subsystems via review articles and detailed analysis of the collection of genomes. These individuals can define the abstract subsystems and add most genomes to the emerging spreadsheets, but not without error. They are necessarily far less skilled than experts who have invested tens of years in study of specific subsystems. These initial subsystems will have many uses. They can be used to enhance sets of curated protein families, to clarify identification of gene starts, and to develop a consistent set of annotations. They will form the basis of informal metabolic reconstructions, and will be used to support the development of formal metabolic reconstructions. However, given the relative lack of expertise of these initial annotators and the fact that they will seldom have access to the wet lab facilities needed to remove ambiguities in assignments, errors will inevitably remain. ==== Stage 2: The Use of True Experts and the Wet Lab to Refine the Encodings ==== The second stage will involve the gradual refinement and enhancement of the original subsystem encodings by domain experts. Almost every subsystem spreadsheet makes it clear that numerous detailed questions remain to be answered. These questions relate to correcting gene calls, correction of frameshifts, refining function assignments, and removing ambiguities (either via bioinformatics based analysis or through actual wet lab efforts). The participation of domain experts will be critical, but it seems most likely that a relatively small set will choose to get involved until the utility of the approach becomes obvious. We already have some domain experts (in translation, transcription, and a limited number of metabolic subsystems) participating in the effort. We believe that this number will grow rapidly over the next 2-3 years. It should be emphasized that upon completion of step 2 we will have accurate annotations and a solid foundation for the construction of stoichiometric matrices. ==== Stage 3: Understanding the Evolutionary History of the Genes within the Subsystem ==== The third stage involves determination of the evolutionary history of the genes within the subsystem. To understand what this involves and the utility of this type of analysis, we must simply recommend two papers by the team led by Roy Jensen: Ancient origin of the tryptophan operon and the dynamics of evolutionary change by Xie, Keyhani, Bonner, Jensen, Microbiol Mol Biol Rev. 2003 Sep;67(3):303-42 Inter-genomic displacement via lateral transfer of bacterial trp operons in an overall context of vertical genealogy, by Xie, Song, Keyhani, Bonner, Jensen, BMC Biology, 2004, 2:15 These papers elegantly display the exact style of analysis required to uncover and clarify the evolutionary history of the relevant genes. Essentially, trees must be built containing all of the genes implementing each specific functional role (multiple trees may be needed for distinct forms). Those trees that display a common topology indicate which columns in the spreadsheet can be used to infer the most probable vertical history of the subsystem. Once the overall history has been clarified, it becomes possible to attempt clarification of horizontal transfers, to reconstruct the history of clusters on the chromosome, and in some cases to tie the analysis to regulatory issues. The effort required to do this style of analysis well is high. While we expect the initial efforts to go slowly, we also expect experience and advances in tools to dramatically reduce the required effort. In any event, it is clear that this stage will not be completed in the next few years, but will undoubtedly stimulate large amounts of related research. === Filling in the Missing Pieces === The encoded subsystems produced by the Project to Annotate 1000 Genomes offer a detailed picture of exactly what components have been identified and are present in each genome. Perhaps as significant, they vividly display exactly what is missing or ambiguous, allowing one to arrive at an accurate inventory of gaps in our understanding. The issue of how best to address these gaps is an integral part of the project. The technology that is emerging is what we refer to as the bioinformatics-driven wet lab. This concept refers to the development of a wet lab that utilizes conventional biochemical and genetic techniques in a framework designed to maximize the overall number of confirmations. It is driven by predictions arising from the analysis of subsystems, and it targets a prioritized list of conjectures. That is, the explicit goal is to fill in as many gaps and remove as many ambiguities as possible for resources consumed. Although it is inconceivable that one experimental group would be able to assess all of the functional predictions, we believe that integrating an experimental component into our annotation/modeling effort will directly support our main goal. In addition to verification of key predictions and removal of central ambiguities, it will validate the overall approach and set an example for other groups worldwide. === The Project to Develop 1000 Stoichiometric Matrices === We believe that the informal metabolic reconstructions are of substantial value by themselves. Indeed, numerous applications are quite obvious. However, they are not enough to support quantitative modeling. Whole genome modeling will require development of stoichiometric matrices, an effort that will pay many dividends. The most immediate payout is as quality control on the informal metabolic reconstruction. Just as the use of subsystems imposes a critical set of consistency checks on the assignment of function to genes, an attempt to develop an internally consistent reaction network imposes a strong consistency check on both the annotations and assertions of the presence of specific subsystems. Over the last 4-5 years, the success of stoichiometric modeling has set the stage for large-scale employment of the technology. The key limiting factor is the development of the stoichiometric matrix itself. This is a time-consuming task that frequently requires on the order of a year for a skilled practitioner. Many actual modeling efforts have foundered on just the technical difficulties in producing this basic datum. Bernhard Palsson has pioneered much of the key research that has led to the recent successes. Spending large amounts of effort, his team has built a very few of these stoichiometric matrices, iteratively improving their accuracy. They have successfully used these matrices to support initial modeling efforts on the organisms, and the results have gained international recognition. Palsson�s team originated the The Project to Produce 1000 Stoichiometric Matrices, and they will play the lead role in converting the informal metabolic reconstructions into formal reconstructions and produce the matrices. The team at FIG and Argonne National Laboratory will participate in the effort, coordinating closely with Palsson�s team. At this point, the Palsson team and the teams at FIG, ANL, and The Burnham Institute are all working on issues relating to tools to automate the generation of matrices from informal metabolic reconstructions. === The Participants === We expect participants in both projects from many institutions worldwide, probably with both academic and commercial interests. Initially, it is likely that the effort will be led from FIG, ANL and Palsson�s team at UCSD. We are planning on Roy Jensen playing a role relating to quality control and development of tools to support Stage 3 analysis. Andrei Osterman from the Burnham Institute will lead wet lab efforts to challenge in silico predictions. If the effort is successful, we would hope to stimulate numerous research efforts worldwide, and we welcome broad participation. Ultimately, leadership and participation will broaden rapidly, if the effort is successful. === A Proposed Schedule === Let us begin by estimating the point at which 1000 genomes will become available. One simple approach would go as follows: The number of genomes will double approximately every 18 months. We now have about 300 more-or-less complete genomes. Therefore, we should have approximately 1000 genomes in just a bit under 3 years (by sometime in 2007) There is a great deal in this analysis that is far from certain. However, let us use this estimate as a working hypothesis. ==== 2005 ==== During 2005, Stage 1 will be completed for the vast majority of subsystems. Stage 2 will be initiated for 30-50 subsystems. Less than 10 will move deeply into stage 3. We will actively attempt to produce 10-15 stoichiometric matrices. We will focus on diverse organisms of interest to DOE and a set of gram-positive pathogens. We will begin a detailed review for quality assurance by a small number of expert biochemists and microbiologists. We expect wet lab confirmations to begin, but this is one area in which funding plays an essential role. We expect funding to support targeted confirmation/rejection of the numerous conjectures arising from the bioinformatics to begin in 2005-2006. It is possible to fairly accurately predict the potential flow of confirmations, but we cannot predict available funding. We believe that the bioinformatics-driven wet lab, in which conjectures are prioritized and grouped, would allow a relatively small group (of 3-4 postdocs and technician) to characterize up to 50 novel gene families encoding the most important functional roles in central metabolic subsystems of diverse organisms per year. ==== 2006 ==== During 2006, the vast majority of subsystems will enter Stage 2. We will attempt to move a large number into Stage 3 (this is truly difficult to predict; it depends hugely on success with the early attempts, our ability to reduce the required effort, and the research aims of the participants). We would plan on completing at least 200 more stoichiometric matrices. If the wet lab component of the effort is fully functional, we would expect a steady stream of confirmations, and (based on our past experience) we would project roughly that 75-90% of the tested conjectures will be validated. ==== 2007 ==== During 2007 we would plan on pushing Stage 2 and 3 analysis as far as possible. We believe that we will have the subsystems needed to cover the vast majority of well understood subsystems and many that are not well understood. We would plan on completing initial stoichiometric matrices for several hundred more genomes. Since the majority of the genomes will not become available until this year, of necessity many of the stoichiometric matrices will not be reasonably complete before sometime in 2008 or 2009. If the wet lab component of the effort is fully functional, we would expect the stream of successful conjectures to stimulate numerous labs to join the effort. Ultimately, the role of the wet lab component that is tightly-coupled to the project is to demonstrate the huge improvement in efficiency that can be attained by coupling the wet lab effort to well-chosen, targeted conjectures generated from the subsystems. === A Short Note on the Analysis of Environmental Samples === It is becoming clear that analysis of environmental samples will become increasingly significant. Consider a framework in which we have 1000 genomes and detailed informal metabolic reconstructions for all of them. We believe that, given a substantial environmental sample, it will be possible to produce accurate estimates of which organisms are present (where an "organism" in this context should probably be viewed as "some organism within a very constrained phylogenetic neighborhood"), it will be possible to produce fairly precise estimates of the metabolism of the organisms believed to be present, and it will be possible to compared the predicted metabolism with the actual enzymes detected in the environmental sample. The hope is clearly that we will be able to make accurate estimates, given 1000 well-annotated genomes. == Summary == The value of a collection of 1000 genomes depends directly on the quality of the annotations, the corresponding metabolic reconstructions, and the extent to which the foundations of modeling have been established. The Project to Annotate 1000 Genomes is based directly on the notion of building a collection of carefully created and curated subsystems. The fact that the individuals who encode these subsystems annotate the same subsystem over a broad collection of genomes allows them to gain an understanding of detailed variation and at least a minimal grasp of the review literature. They will be annotating genes for which they develop some detailed familiarity. We place this technology in direct opposition to the existing approaches in which individuals annotate complete genomes (assuring an almost complete lack of familiarity with the majority of genes being annotated), and automated pipelines are badly limited by the ambiguities and errors in existing annotations. The Project to Produce 1000 Stoichiometric Matrices has the potential of laying the foundations for quantitative modeling. Many, if not most, existing modeling efforts are dramatically hampered by the fact that very, very few stoichiometric matrices now exist, and the cost of developing more using existing approaches is quite high. The development of a wet lab component that challenges a carefully prioritized set of conjectures flowing from both the subsystems analysis and the initial modeling based on quantitative modeling is essential. It will confirm the relative efficiency of this approach (which might reasonably be characterized as "picking the low-hanging fruit"), and in the process establish a paradigm that directly challenges the more common approach to establishing priorities. We claim to understand the key technology needed to develop high-throughput development of annotations, metabolic reconstructions, and stoichiometric matrices. By the summer of 2005, this should be completely obvious. bc3db306cee8ea838bb1bf6ebeac64e3c347a0e4 0 1384 1516 2006-11-02T14:24:42Z Mkubal 15 wikitext text/x-wiki work in progress 84c6911ace997b238a26725c5487904a175e003d 1517 1516 2006-11-02T14:45:23Z Mkubal 15 wikitext text/x-wiki General features of SeedViewer For a description of how to use the features on the different Seed Viewer pages, please visit the links below: [[#SeedViewer_Search| Search on Home page]] [[#SeedViewer_Organism| Organism page]] [[#SeedViewer_Search| Annotation page]] [[#SeedViewer_Functional_Role| Functional Role page]] [[#SeedViewer_Subsystem| Subsystem page]] For tutorials on accomplishing specific tasks, please visit the link below: [[#SeedViewer_Tutorial| Tutorials]] 8c9741ae2eaf247d2bc19f9a2fd2e6f767b90a84 1518 1517 2006-11-02T14:50:55Z Mkubal 15 wikitext text/x-wiki General features of SeedViewer For a description of how to use the features on the different Seed Viewer pages, please visit the links below: == [[#SeedViewer_Search| Search on Home page]] [[#SeedViewer_Organism| Organism page]] [[#SeedViewer_Search| Annotation page]] [[#SeedViewer_Functional_Role| Functional Role page]] [[#SeedViewer_Subsystem| Subsystem page]] = For tutorials on accomplishing specific tasks, please visit the link below: == [[#SeedViewer_Tutorial| Tutorials]] 41d5b9c474ad5c87e73832f22cd666d0f6c0a56f 1519 1518 2006-11-02T14:59:16Z Mkubal 15 wikitext text/x-wiki General features of SeedViewer For a description of how to use the features on the different Seed Viewer pages, please follow the links below: :[[#SeedViewer_Search| Search on Home page]] :[[#SeedViewer_Organism| Organism page]] :[[#SeedViewer_Search| Annotation page]] :[[#SeedViewer_Functional_Role| Functional Role page]] :[[#SeedViewer_Subsystem| Subsystem page]] For tutorials on accomplishing specific tasks, please follow the link below: :[[#SeedViewer_Tutorial| Tutorials]] 9c641fbd1a8b36de5c9860922647bf45fe1e2e1f 1520 1519 2006-11-02T15:00:22Z Mkubal 15 wikitext text/x-wiki ===General features of SeedViewer=== ===For a description of how to use the features on the different Seed Viewer pages, please follow the links below:=== :[[#SeedViewer_Search| Search on Home page]] :[[#SeedViewer_Organism| Organism page]] :[[#SeedViewer_Search| Annotation page]] :[[#SeedViewer_Functional_Role| Functional Role page]] :[[#SeedViewer_Subsystem| Subsystem page]] ===For tutorials on accomplishing specific tasks, please follow the link below:=== :[[#SeedViewer_Tutorial| Tutorials]] e514a2ca49c03ac7fe838198666e6c8bb541d55b 1521 1520 2006-11-02T15:04:03Z Mkubal 15 wikitext text/x-wiki ===General features of SeedViewer=== ===For a description of how to use the features on the different Seed Viewer pages, please follow the links below:=== :[[#SeedViewer_Search| Home page]] :[[#SeedViewer_Organism| Organism page]] :[[#SeedViewer_Search| Annotation page]] :[[#SeedViewer_Functional_Role| Functional Role page]] :[[#SeedViewer_Subsystem| Subsystem page]] ===For tutorials on accomplishing specific tasks, please follow the link below:=== :[[#SeedViewer_Tutorial| Tutorials]] c68e70e1bffb12b4975a826db9c3ea5aa9031fd5 1522 1521 2006-11-02T15:04:44Z Mkubal 15 wikitext text/x-wiki ===General features of SeedViewer=== ===For a description of how to use the features on the different Seed Viewer pages, please follow the links below:=== :[[#SeedViewer_Home| Home page]] :[[#SeedViewer_Organism| Organism page]] :[[#SeedViewer_Search| Annotation page]] :[[#SeedViewer_Functional_Role| Functional Role page]] :[[#SeedViewer_Subsystem| Subsystem page]] ===For tutorials on accomplishing specific tasks, please follow the link below:=== :[[#SeedViewer_Tutorial| Tutorials]] 28d165db0ea18744960bb7a81491ed04f437ceb4 1524 1522 2006-11-02T15:11:28Z Mkubal 15 wikitext text/x-wiki ===General features of SeedViewer=== ===For a description of how to use the features on the different Seed Viewer pages, please follow the links below:=== :[[SeedViewer_Home| Home page]] :[[#SeedViewer_Organism| Organism page]] :[[#SeedViewer_Search| Annotation page]] :[[#SeedViewer_Functional_Role| Functional Role page]] :[[#SeedViewer_Subsystem| Subsystem page]] ===For tutorials on accomplishing specific tasks, please follow the link below:=== :[[#SeedViewer_Tutorial| Tutorials]] 30d95fa82d389df530c43538481c9a5e0384563e 1525 1524 2006-11-02T15:12:15Z Mkubal 15 wikitext text/x-wiki ===General features of SeedViewer=== ===For a description of how to use the features on the different Seed Viewer pages, please follow the links below:=== :[[SeedViewer_Home| Home page]] :[[SeedViewer_Organism| Organism page]] :[[SeedViewer_Search| Annotation page]] :[[SeedViewer_Functional_Role| Functional Role page]] :[[SeedViewer_Subsystem| Subsystem page]] ===For tutorials on accomplishing specific tasks, please follow the link below:=== :[[SeedViewer_Tutorial| Tutorials]] b701c30a89b4c065ca8fdc5e6175646b38871daa 1540 1525 2006-11-02T20:29:42Z Mkubal 15 wikitext text/x-wiki ===General Features and Conventions of SeedViewer=== :Tool tips - [?] indicates a tool tip will appear when hovered above with the mouse. Underlined [?] indicates a clickable tool tip <br> :that also links into a wiki page for a more detailed explanation<br> :Text Entry Boxes - if the text box has a pulldown menu beneath it, as text is entered in the box the menu will be updated with only items<br> that match or contain the entered text.<br> :Sorting Table Entries - alpahnumerically sort or reverse sort with the respective triangle in a column header<br> :Browsing Table Entries - use the next>> and last>> links to quickly browse tables with more than 10 rows ===For a description of how to use the features on the different Seed Viewer pages, please follow the links below:=== :[[SeedViewer_Home| Home page]] :[[SeedViewer_Organism| Organism page]] :[[SeedViewer_Search| Annotation page]] :[[SeedViewer_Functional_Role| Functional Role page]] :[[SeedViewer_Subsystem| Subsystem page]] ===For tutorials on accomplishing specific tasks, please follow the link below:=== :[[SeedViewer_Tutorial| Tutorials]] 1431561fce27fdef53354942ba21e0d686ae89bf 1541 1540 2006-11-02T20:30:46Z Mkubal 15 wikitext text/x-wiki ===General Features and Conventions of SeedViewer=== :Tool tips - [?] indicates a tool tip will appear when hovered above with the mouse. Underlined [?] indicates a clickable tool tip <br> :that also links into a wiki page for a more detailed explanation :Text Entry Boxes - if the text box has a pulldown menu beneath it, as text is entered in the box the menu will be updated with only items<br> :that match or contain the entered text. :Sorting Table Entries - alpahnumerically sort or reverse sort with the respective triangle in a column header :Browsing Table Entries - use the next>> and last>> links to quickly browse tables with more than 10 rows ===For a description of how to use the features on the different Seed Viewer pages, please follow the links below:=== :[[SeedViewer_Home| Home page]] :[[SeedViewer_Organism| Organism page]] :[[SeedViewer_Search| Annotation page]] :[[SeedViewer_Functional_Role| Functional Role page]] :[[SeedViewer_Subsystem| Subsystem page]] ===For tutorials on accomplishing specific tasks, please follow the link below:=== :[[SeedViewer_Tutorial| Tutorials]] 2ded5ab12adc2d9c2eb40676ce30ddce808f5185 1551 1541 2006-11-03T20:46:03Z Mkubal 15 wikitext text/x-wiki ===General Features and Conventions of SeedViewer=== :Tool tips - [?] indicates a tool tip will appear when hovered above with the mouse. Underlined [?] indicates a clickable tool tip <br> :that also links into a wiki page for a more detailed explanation :Text Entry Boxes - if the text box has a pulldown menu beneath it, as text is entered in the box the menu will be updated with only items<br> :that match or contain the entered text. :Sorting Table Entries - alpahnumerically sort or reverse sort with the respective triangle in a column header :Browsing Table Entries - use the next>> and last>> links to quickly browse tables with more than 10 rows ===For a description of how to use the features on the different Seed Viewer pages, please follow the links below:=== :[[SeedViewer_Home| Home page]] :[[SeedViewer_Organism| Organism page]] :[[SeedViewer_Annotation| Annotation page]] :[[SeedViewer_Functional_Role| Functional Role page]] :[[SeedViewer_Subsystem| Subsystem page]] ===For tutorials on accomplishing specific tasks, please follow the link below:=== :[[SeedViewer_Tutorial| Tutorials]] 07af580a04a852cac182c5be0029a254c553b342 0 1385 1523 2006-11-02T15:11:02Z Mkubal 15 wikitext text/x-wiki test a94a8fe5ccb19ba61c4c0873d391e987982fbbd3 1526 1523 2006-11-02T15:28:47Z Mkubal 15 wikitext text/x-wiki The SEED Viewer's home page provides 4 different perspectives on searching to help you effciently access the data in the SEED. 'Text Search' is the default search. Enter a key word or phrase in the text box and click the button to the right of the text box. By clicking on 'BLAST Search', 'Subsystems' or 'Organisms' you can change your search perspective.<br> Notice that the text on button to the right of the text entry box will change after clicking on one of these perspectives. da129d959ea62e5fa1036e9393a3508bd552abca 1527 1526 2006-11-02T18:42:59Z Mkubal 15 wikitext text/x-wiki The SEED Viewer's home page provides 4 different perspectives on searching to help you effciently access the data in the SEED. By clicking on 'BLAST Search', 'Subsystems' or 'Organisms' you can change your search perspective.<br> Notice that the text on button to the right of the text entry box will change after clicking on one of these perspectives. Text Search<br> :This is the default search option. Enter a key word or phrase in the text box and click the button to the right of the text box.<br> :This search cover features, functional roles and subsystems. :If you check the 'quick search' option, the results will be limited to features associated with a functional role in a subsystem. Blast Search<br> : Enter a DNA or amino acid sequence d8862f66131a9147857f61dc7a9b26776aab4689 1528 1527 2006-11-02T18:50:02Z Mkubal 15 wikitext text/x-wiki The SEED Viewer's home page provides 4 different perspectives on searching to help you effciently access the data in the SEED. By clicking on 'BLAST Search', 'Subsystems' or 'Organisms' you can change your search perspective.<br> Notice that the text on button to the right of the text entry box will change after clicking on one of these perspectives. Text Search<br> :This is the default search option. Enter a key word or phrase in the text box and click the button to the right of the text box.<br> :This search cover features, functional roles and subsystems. :If you check the 'quick search' option, the results will be limited to features associated with a functional role in a subsystem. : Blast Search<br> : Enter a DNA or amino acid sequence, and select a genome from the pulldown menu above the text box. You must select a genome.<br> : Then click the 'Blast Search' button to the right of the genome pulldown menu. : The results will be in typical Blast output format and include PEG IDs that are linked to an Annotation page in the SEED Viewer. 034c568d0cb0ffcb8a20cc9a9a9f17e387914d11 1529 1528 2006-11-02T19:12:21Z Mkubal 15 wikitext text/x-wiki The SEED Viewer's home page provides 4 different perspectives on searching to help you effciently access the data in the SEED.<br> By clicking on 'BLAST Search', 'Subsystems' or 'Organisms' you can change your search perspective.<br> Notice that the text on button to the right of the text entry box will change after clicking on one of these perspectives. Text Search<br> :This is the default search option. Enter a key word or phrase in the text box and click the button to the right of the text box.<br> :This search cover features, functional roles and subsystems. :If you check the 'quick search' option, the results will be limited to features associated with a functional role in a subsystem. :The results of the search will be displayed in 2 tables, a Functional Role table and Subsystem table. The number of hits associated <br> :with a functional role will appear above the Functional Role table. To browse the results quickly use the next >> and last >> links. :The columns in both tables can be alpanumerically sorted and reverse sorted by clicking on the respective triangle in the column header.<br> Blast Search<br> : Enter a DNA or amino acid sequence, and select a genome from the pulldown menu above the text box. You must select a genome.<br> : Then click the 'Blast Search' button to the right of the genome pulldown menu. : The results will be in typical Blast output format and include PEG IDs that are linked to an Annotation page in the SEED Viewer. Organism Search<br> :Selecting this option provides an alphabetized pulldown menu of genomes in the SEED and also a text entry box.<br> :Notice as you type in text entry box the pulldown menu is automatically updated with genomes that contain the entered text,<br> : not just at the beginning of the genome. 9545b6ee83fbf60177f4b2bb614cea634357b5f0 1530 1529 2006-11-02T19:13:27Z Mkubal 15 wikitext text/x-wiki The SEED Viewer's home page provides 4 different perspectives on searching to help you effciently access the data in the SEED.<br> By clicking on 'BLAST Search', 'Subsystems' or 'Organisms' you can change your search perspective.<br> Notice that the text on button to the right of the text entry box will change after clicking on one of these perspectives. Text Search<br> :This is the default search option. Enter a key word or phrase in the text box and click the button to the right of the text box.<br> :This search cover features, functional roles and subsystems. :If you check the 'quick search' option, the results will be limited to features associated with a functional role in a subsystem. :The results of the search will be displayed in 2 tables, a Functional Role table and Subsystem table. The number of hits associated <br> :with a functional role will appear above the Functional Role table. To browse the results quickly use the next >> and last >> links. :The columns in both tables can be alphanumerically sorted and reverse sorted by clicking on the respective triangle in the column header.<br> Blast Search<br> : Enter a DNA or amino acid sequence, and select a genome from the pulldown menu above the text box. You must select a genome.<br> : Then click the 'Blast Search' button to the right of the genome pulldown menu. : The results will be in typical Blast output format and include PEG IDs that are linked to an Annotation page in the SEED Viewer. Organism Search<br> :Selecting this option provides an alphabetized pulldown menu of genomes in the SEED and also a text entry box.<br> :Notice as you type in text entry box the pulldown menu is automatically updated with genomes that contain the entered text,<br> : not just at the beginning of the genome. bf0a4deae89b9cce36fcb674aab652052799ed3c 1531 1530 2006-11-02T19:14:42Z Mkubal 15 wikitext text/x-wiki The SEED Viewer's home page provides 4 different perspectives on searching to help you effciently access the data in the SEED.<br> By clicking on 'BLAST Search', 'Subsystems' or 'Organisms' you can change your search perspective.<br> Notice that the text on button to the right of the text entry box will change after clicking on one of these perspectives. Text Search<br> :This is the default search option. Enter a key word or phrase in the text box and click the button to the right of the text box.<br> :This search cover features, functional roles and subsystems. :If you check the 'quick search' option, the results will be limited to features associated with a functional role in a subsystem. :The results of the search will be displayed in 2 tables, a Functional Role table and Subsystem table. The number of hits associated <br> :with a functional role will appear above the Functional Role table. To browse the results quickly use the next >> and last >> links. :The columns in both tables can be alphanumerically sorted and reverse sorted by clicking on the respective triangle in the column header.<br> Blast Search<br> : Enter a DNA or amino acid sequence, and select a genome from the pulldown menu above the text box. You must select a genome.<br> : Then click the 'Blast Search' button to the right of the genome pulldown menu. : The results will be in typical Blast output format and include PEG IDs that are linked to an Annotation page in the SEED Viewer. Organism Search<br> :Selecting this option provides an alphabetized pulldown menu of genomes in the SEED and also a text entry box.<br> :Notice as you type in text entry box the pulldown menu is automatically updated with genomes that contain the entered text,<br> :and not just matching at the beginning of the genome. bb3ef8086cdb9fa11c8d9d8d66f3d6b0b8f19b74 1532 1531 2006-11-02T19:22:32Z Mkubal 15 wikitext text/x-wiki The SEED Viewer's home page provides 4 different perspectives on searching to help you effciently access the data in the SEED.<br> By clicking on 'BLAST Search', 'Subsystems' or 'Organisms' you can change your search perspective.<br> Notice that the text on button to the right of the text entry box will change after clicking on one of these perspectives. Text Search<br> :This is the default search option. Enter a key word or phrase in the text box and click the button to the right of the text box.<br> :This search cover features, functional roles and subsystems. :If you check the 'quick search' option, the results will be limited to features associated with a functional role in a subsystem. :The results of the search will be displayed in 2 tables, a Functional Role table and Subsystem table. The number of hits associated <br> :with a functional role will appear above the Functional Role table. To browse the results quickly use the next >> and last >> links. :The columns in both tables can be alphanumerically sorted and reverse sorted by clicking on the respective triangle in the column header.<br> Blast Search<br> : Enter a DNA or amino acid sequence, and select a genome from the pulldown menu above the text box. You must select a genome.<br> : Then click the 'Blast Search' button to the right of the genome pulldown menu. : The results will be in typical Blast output format and include PEG IDs that are linked to an Annotation page in the SEED Viewer. Subsystems Search<br> :Selecting this option provides an alphanumerically sorted pulldown menu of subsystems in the SEED and also a text entry box.<br> :Notice as you type in text entry box the pulldown menu is automatically updated with subsystems that contain the entered text,<br> :and not just matching at the beginning of the subsystem name. :After selecting a subsystem, clicking the 'View Subsystem' button will take you a Subsystem page in the SEED Viewer. Organism Search<br> :Selecting this option provides an alphabetized pulldown menu of genomes in the SEED and also a text entry box.<br> :Notice as you type in text entry box the pulldown menu is automatically updated with genomes that contain the entered text,<br> :and not just matching at the beginning of the genome. :After selecting an organism, clicking the 'View Organism' button will take you an organism page in the SEED Viewer. 50cec650064fde40b9db4be4ffc182174c165af9 1533 1532 2006-11-02T19:23:39Z Mkubal 15 wikitext text/x-wiki The SEED Viewer's home page provides 4 different perspectives on searching to help you effciently access the data in the SEED.<br> By clicking on 'Text Search','BLAST Search', 'Subsystems' or 'Organisms' you can change your search perspective.<br> Notice that the text on button to the right of the text entry box will change after clicking on one of these perspectives. Text Search<br> :This is the default search option. Enter a key word or phrase in the text box and click the button to the right of the text box.<br> :This search cover features, functional roles and subsystems. :If you check the 'quick search' option, the results will be limited to features associated with a functional role in a subsystem. :The results of the search will be displayed in 2 tables, a Functional Role table and Subsystem table. The number of hits associated <br> :with a functional role will appear above the Functional Role table. To browse the results quickly use the next >> and last >> links. :The columns in both tables can be alphanumerically sorted and reverse sorted by clicking on the respective triangle in the column header.<br> Blast Search<br> : Enter a DNA or amino acid sequence, and select a genome from the pulldown menu above the text box. You must select a genome.<br> : Then click the 'Blast Search' button to the right of the genome pulldown menu. : The results will be in typical Blast output format and include PEG IDs that are linked to an Annotation page in the SEED Viewer. Subsystems Search<br> :Selecting this option provides an alphanumerically sorted pulldown menu of subsystems in the SEED and also a text entry box.<br> :Notice as you type in text entry box the pulldown menu is automatically updated with subsystems that contain the entered text,<br> :and not just matching at the beginning of the subsystem name. :After selecting a subsystem, clicking the 'View Subsystem' button will take you a Subsystem page in the SEED Viewer. Organism Search<br> :Selecting this option provides an alphabetized pulldown menu of genomes in the SEED and also a text entry box.<br> :Notice as you type in text entry box the pulldown menu is automatically updated with genomes that contain the entered text,<br> :and not just matching at the beginning of the genome. :After selecting an organism, clicking the 'View Organism' button will take you an organism page in the SEED Viewer. 99f69c8bf315a26e9d5e92baf03512755bdea340 1534 1533 2006-11-02T19:24:45Z Mkubal 15 wikitext text/x-wiki The SEED Viewer's home page provides 4 different perspectives on searching to help you effciently access the data in the SEED.<br> By clicking on 'Text Search','BLAST Search', 'Subsystems' or 'Organisms' you can change your search perspective.<br> Notice that the text on button to the right of the text entry box will change after clicking on one of these perspectives. Text Search<br> :This is the default search option. Enter a key word or phrase in the text box and click the 'Text Search' button to the right of the text box.<br> :This search cover features, functional roles and subsystems. :If you check the 'quick search' option, the results will be limited to features associated with a functional role in a subsystem. :The results of the search will be displayed in 2 tables, a Functional Role table and Subsystem table. The number of hits associated <br> :with a functional role will appear above the Functional Role table. To browse the results quickly use the next >> and last >> links. :The columns in both tables can be alphanumerically sorted and reverse sorted by clicking on the respective triangle in the column header.<br> Blast Search<br> : Enter a DNA or amino acid sequence, and select a genome from the pulldown menu above the text box. You must select a genome.<br> : Then click the 'Blast Search' button to the right of the genome pulldown menu. : The results will be in typical Blast output format and include PEG IDs that are linked to an Annotation page in the SEED Viewer. Subsystems Search<br> :Selecting this option provides an alphanumerically sorted pulldown menu of subsystems in the SEED and also a text entry box.<br> :Notice as you type in text entry box the pulldown menu is automatically updated with subsystems that contain the entered text,<br> :and not just matching at the beginning of the subsystem name. :After selecting a subsystem, clicking the 'View Subsystem' button will take you a Subsystem page in the SEED Viewer. Organism Search<br> :Selecting this option provides an alphabetized pulldown menu of genomes in the SEED and also a text entry box.<br> :Notice as you type in text entry box the pulldown menu is automatically updated with genomes that contain the entered text,<br> :and not just matching at the beginning of the genome. :After selecting an organism, clicking the 'View Organism' button will take you an organism page in the SEED Viewer. 0ba23e439440d7de439dbdbe769d35a830b978f7 1535 1534 2006-11-02T19:36:37Z Mkubal 15 wikitext text/x-wiki ===Counts of Genomes in the SEED=== The SEED contains archeal, bacterial, eukaryal, and viral genomes, as well as environmental samples.<br> A box on the top right of the page provides a current total and complete count of each type. ===Searching=== The SEED Viewer's home page provides 4 different perspectives on searching to help you effciently access the data in the SEED.<br> By clicking on 'Text Search','BLAST Search', 'Subsystems' or 'Organisms' you can change your search perspective.<br> Notice that the text on button to the right of the text entry box will change after clicking on one of these perspectives. Text Search<br> :This is the default search option. Enter a key word or phrase in the text box and click the 'Text Search' button to the right of the text box.<br> :This search cover features, functional roles and subsystems. :If you check the 'quick search' option, the results will be limited to features associated with a functional role in a subsystem. :The results of the search will be displayed in 2 tables, a Functional Role table and Subsystem table. The number of hits associated <br> :with a functional role will appear above the Functional Role table. To browse the results quickly use the next >> and last >> links. :The columns in both tables can be alphanumerically sorted and reverse sorted by clicking on the respective triangle in the column header.<br> Blast Search<br> : Enter a DNA or amino acid sequence, and select a genome from the pulldown menu above the text box. You must select a genome.<br> : Then click the 'Blast Search' button to the right of the genome pulldown menu. : The results will be in typical Blast output format and include PEG IDs that are linked to an Annotation page in the SEED Viewer. Subsystems Search<br> :Selecting this option provides an alphanumerically sorted pulldown menu of subsystems in the SEED and also a text entry box.<br> :Notice as you type in text entry box the pulldown menu is automatically updated with subsystems that contain the entered text,<br> :and not just matching at the beginning of the subsystem name. :After selecting a subsystem, clicking the 'View Subsystem' button will take you a Subsystem page in the SEED Viewer. Organism Search<br> :Selecting this option provides an alphabetized pulldown menu of genomes in the SEED and also a text entry box.<br> :Notice as you type in text entry box the pulldown menu is automatically updated with genomes that contain the entered text,<br> :and not just matching at the beginning of the genome. :After selecting an organism, clicking the 'View Organism' button will take you an organism page in the SEED Viewer. 86f6dfa3bc3eb56f0edb786662d0088c3921291d 1536 1535 2006-11-02T19:37:21Z Mkubal 15 wikitext text/x-wiki ===Counts of Genomes in the SEED=== The SEED contains archeal, bacterial, eukaryal, and viral genomes, as well as environmental samples.<br> A box on the top right of the home page provides a current total and complete count of each type. ===Searching=== The SEED Viewer's home page provides 4 different perspectives on searching to help you effciently access the data in the SEED.<br> By clicking on 'Text Search','BLAST Search', 'Subsystems' or 'Organisms' you can change your search perspective.<br> Notice that the text on button to the right of the text entry box will change after clicking on one of these perspectives. Text Search<br> :This is the default search option. Enter a key word or phrase in the text box and click the 'Text Search' button to the right of the text box.<br> :This search cover features, functional roles and subsystems. :If you check the 'quick search' option, the results will be limited to features associated with a functional role in a subsystem. :The results of the search will be displayed in 2 tables, a Functional Role table and Subsystem table. The number of hits associated <br> :with a functional role will appear above the Functional Role table. To browse the results quickly use the next >> and last >> links. :The columns in both tables can be alphanumerically sorted and reverse sorted by clicking on the respective triangle in the column header.<br> Blast Search<br> : Enter a DNA or amino acid sequence, and select a genome from the pulldown menu above the text box. You must select a genome.<br> : Then click the 'Blast Search' button to the right of the genome pulldown menu. : The results will be in typical Blast output format and include PEG IDs that are linked to an Annotation page in the SEED Viewer. Subsystems Search<br> :Selecting this option provides an alphanumerically sorted pulldown menu of subsystems in the SEED and also a text entry box.<br> :Notice as you type in text entry box the pulldown menu is automatically updated with subsystems that contain the entered text,<br> :and not just matching at the beginning of the subsystem name. :After selecting a subsystem, clicking the 'View Subsystem' button will take you a Subsystem page in the SEED Viewer. Organism Search<br> :Selecting this option provides an alphabetized pulldown menu of genomes in the SEED and also a text entry box.<br> :Notice as you type in text entry box the pulldown menu is automatically updated with genomes that contain the entered text,<br> :and not just matching at the beginning of the genome. :After selecting an organism, clicking the 'View Organism' button will take you an organism page in the SEED Viewer. 7baeebefe7cacd2194f962f037458284676375d7 1537 1536 2006-11-02T19:58:44Z Mkubal 15 wikitext text/x-wiki ===Counts of Genomes in the SEED=== The SEED contains archeal, bacterial, eukaryal, and viral genomes, as well as environmental samples.<br> A box on the top right of the home page provides a current total and complete count of each type. ===Searching=== The SEED Viewer's home page provides 4 different perspectives on searching to help you effciently access the data in the SEED.<br> By clicking on 'Text Search','BLAST Search', 'Subsystems' or 'Organisms' you can change your search perspective.<br> Notice that the text on button to the right of the text entry box will change after clicking on one of these perspectives. Text Search<br> :This is the default search option. Enter a key word or phrase in the text box and click the 'Text Search' button to the right of the text box.<br> :The search will treat the entered text as a regular expression and match strings and substrings found in functional roles, subsystems and features. :The results of the search will be displayed in up to 3 tables, a Functional Role table, Subsystem table and Features table.<br> :The number of hits associated with a functional role will appear above the Functional Role table. <br> :The number of features returned is limited to 100. <br> :To browse the results quickly use the next >> and last >> links. :The columns in all tables can be alphanumerically sorted and reverse sorted by clicking on the respective triangle in a column header.<br> :If you check the 'quick search' option, the results will be limited to functionals role in a subsystem. Blast Search<br> : Enter a DNA or amino acid sequence, and select a genome from the pulldown menu above the text box. You must select a genome.<br> : Then click the 'Blast Search' button to the right of the genome pulldown menu. : The results will be in typical Blast output format and include PEG IDs that are linked to an Annotation page in the SEED Viewer. Subsystems Search<br> :Selecting this option provides an alphanumerically sorted pulldown menu of subsystems in the SEED and also a text entry box.<br> :Notice as you type in text entry box the pulldown menu is automatically updated with subsystems that contain the entered text,<br> :and not just matching at the beginning of the subsystem name. :After selecting a subsystem, clicking the 'View Subsystem' button will take you a Subsystem page in the SEED Viewer. Organism Search<br> :Selecting this option provides an alphabetized pulldown menu of genomes in the SEED and also a text entry box.<br> :Notice as you type in text entry box the pulldown menu is automatically updated with genomes that contain the entered text,<br> :and not just matching at the beginning of the genome. :After selecting an organism, clicking the 'View Organism' button will take you an organism page in the SEED Viewer. 07214fd7784221dbf14489bd036a80a85f0fe1ff 1538 1537 2006-11-02T19:59:42Z Mkubal 15 wikitext text/x-wiki ===Counts of Genomes in the SEED=== The SEED contains archeal, bacterial, eukaryal, and viral genomes, as well as environmental samples.<br> A box on the top right of the home page provides a current total and complete count of each type. ===Searching=== The SEED Viewer's home page provides 4 different perspectives on searching to help you effciently access the data in the SEED.<br> By clicking on 'Text Search','BLAST Search', 'Subsystems' or 'Organisms' you can change the search perspective.<br> Notice that the text on button to the right of the text entry box will change after clicking on one of these perspectives. Text Search<br> :This is the default search option. Enter a key word or phrase in the text box and click the 'Text Search' button to the right of the text box.<br> :The search will treat the entered text as a regular expression and match strings and substrings found in functional roles, subsystems and features. :The results of the search will be displayed in up to 3 tables, a Functional Role table, Subsystem table and Features table.<br> :The number of hits associated with a functional role will appear above the Functional Role table. <br> :The number of features returned is limited to 100. <br> :To browse the results quickly use the next >> and last >> links. :The columns in all tables can be alphanumerically sorted and reverse sorted by clicking on the respective triangle in a column header.<br> :If you check the 'quick search' option, the results will be limited to functionals role in a subsystem. Blast Search<br> : Enter a DNA or amino acid sequence, and select a genome from the pulldown menu above the text box. You must select a genome.<br> : Then click the 'Blast Search' button to the right of the genome pulldown menu. : The results will be in typical Blast output format and include PEG IDs that are linked to an Annotation page in the SEED Viewer. Subsystems Search<br> :Selecting this option provides an alphanumerically sorted pulldown menu of subsystems in the SEED and also a text entry box.<br> :Notice as you type in text entry box the pulldown menu is automatically updated with subsystems that contain the entered text,<br> :and not just matching at the beginning of the subsystem name. :After selecting a subsystem, clicking the 'View Subsystem' button will take you a Subsystem page in the SEED Viewer. Organism Search<br> :Selecting this option provides an alphabetized pulldown menu of genomes in the SEED and also a text entry box.<br> :Notice as you type in text entry box the pulldown menu is automatically updated with genomes that contain the entered text,<br> :and not just matching at the beginning of the genome. :After selecting an organism, clicking the 'View Organism' button will take you an organism page in the SEED Viewer. c61cebcb6a94d7b08755c86353cf0321a6648bf1 1539 1538 2006-11-02T20:06:50Z Mkubal 15 wikitext text/x-wiki ===Counts of Genomes in the SEED=== The SEED contains archeal, bacterial, eukaryal, and viral genomes, as well as environmental samples.<br> A box on the top right of the home page provides a current total and complete count of each type. ===Searching=== The SEED Viewer's home page provides 4 different perspectives on searching to help you effciently access the data in the SEED.<br> By clicking on 'Text Search','BLAST Search', 'Subsystems' or 'Organisms' you can change the search perspective.<br> Notice that the text on button to the right of the text entry box will change after clicking on one of these perspectives. Text Search<br> :This is the default search option. Enter a key word or phrase in the text box and click the 'Text Search' button to the right of the text box.<br> :The search will treat the entered text as a regular expression and match strings and substrings found in functional roles, subsystems and features. :The results of the search will be displayed in up to 3 tables, a Functional Role table, Subsystem table and Features table.<br> :The number of hits associated with a functional role will appear above the Functional Role table. <br> :The number of features returned is limited to 100. <br> :To browse the results quickly use the next >> and last >> links. :The columns in all tables can be alphanumerically sorted and reverse sorted by clicking on the respective triangle in a column header.<br> :If you check the 'quick search' option, the results will be limited to functionals role in a subsystem. :In any of the results tables, :clicking on a functional role will take you to a Functional Role page in the SEED Viewer, :clicking on a subsystem will take you to a Subsystem page in the SEED Viewer and :clicking on a PEG ID will take you an Annotation page in the SEED Viewer. Blast Search<br> : Enter a DNA or amino acid sequence, and select a genome from the pulldown menu above the text box. You must select a genome.<br> : Then click the 'Blast Search' button to the right of the genome pulldown menu. : The results will be in typical Blast output format and include PEG IDs that are linked to an Annotation page in the SEED Viewer. Subsystems Search<br> :Selecting this option provides an alphanumerically sorted pulldown menu of subsystems in the SEED and also a text entry box.<br> :Notice as you type in text entry box the pulldown menu is automatically updated with subsystems that contain the entered text,<br> :and not just matching at the beginning of the subsystem name. :After selecting a subsystem, clicking the 'View Subsystem' button will take you a Subsystem page in the SEED Viewer. Organism Search<br> :Selecting this option provides an alphabetized pulldown menu of genomes in the SEED and also a text entry box.<br> :Notice as you type in text entry box the pulldown menu is automatically updated with genomes that contain the entered text,<br> :and not just matching at the beginning of the genome. :After selecting an organism, clicking the 'View Organism' button will take you an organism page in the SEED Viewer. dc859f98e62b57610e50c54960109d65c39993a7 0 1386 1542 2006-11-03T15:58:39Z Mkubal 15 wikitext text/x-wiki Organism Page in SEED Viewer In the green bar at the top of the page adjacent to the homepage symbol is pulldown menu<br> labeled 'This Organism' with the following 4 display options for this page:<br> Overview :The top of page provides summary statistics for this genome including the numbers of subsystems, coding sequences, RNAs and other background information.<br> :A breakdown of the number of PEGs with hypothetical and non-hypothetical function assignments is provided in box in the top right corner of the page.<br> :Adjacent to the Taxonomy ID is the Wikipedia Globe that is linked to the Wikipedia entry for this organism. :On the bottom left of the page a bar graph depicts the percentages of PEGs for this genome that are present in at least one subsystem.<br> :Next to the bar graph a pie chart and accompanying expandable hierarchical tree, color coded to match the pie chart, organizes the subsystems<br> :present in this genome by cellular process. :At every level in the tree the number of PEGs in each category is listed in parentheses. :At the leaves of the tree are links to a Subsytem page in the SEED Viewer. Browse Genome View Features View Reactions 75136cab0b2d93181ada1176a1df82d29cdadc40 1543 1542 2006-11-03T16:54:20Z Mkubal 15 wikitext text/x-wiki Organism Page in SEED Viewer In the green bar at the top of the page adjacent to the homepage symbol is pulldown menu<br> labeled 'This Organism' with the following 4 display options for this page:<br> Overview :The top of page provides summary statistics for this genome including the numbers of subsystems, coding sequences, RNAs and other background information.<br> :A breakdown of the number of PEGs with hypothetical and non-hypothetical function assignments is provided in box in the top right corner of the page.<br> :Adjacent to the Taxonomy ID is the Wikipedia Globe that is linked to the Wikipedia entry for this organism. :On the bottom left of the page a bar graph depicts the percentages of PEGs for this genome that are present in at least one subsystem.<br> :Next to the bar graph a pie chart and accompanying expandable hierarchical tree, color coded to match the pie chart, organizes the subsystems<br> :present in this genome by cellular process. :At every level in the tree the number of PEGs in each category is listed in parentheses. :At the leaves of the tree are links to a Subsytem page in the SEED Viewer. Browse Genome :This display allows a you to walk the chromosome of the selected genome.<br> :. If the genome is not completely assembled, the first contig will be selected. :The window size in terms of number of base pairs can be selected using the 'Window Size' pulldown menu, or the 'zoom in' or 'zoom out' buttons.<br> : The < and > buttons will move the window down or up the chromosome half the window size.<br> :The << and >> buttons will move the window down or up the chromosome a full window size.<br> :Under 'Options' you can select which features are displayed and the number of reading frames. By default the genome browser offers a two frame view of the currently selected organism.<br> :After selecting your options, click the 'Refresh' button to update the page. :On the middle line of the chromosome display you will see features not associated with a reading frame, such as rnas, pathogenicity islands or prophages.<br> :Hover over a feature in the chromosome display for a detailed description. :Clicking an item will take you to the Annotation page in the SEED Viewer for this feature. View Features View Reactions ee17ac67e6ac329d7851aa2ac10721d89522ab5e 1544 1543 2006-11-03T16:55:04Z Mkubal 15 wikitext text/x-wiki Organism Page in SEED Viewer In the green bar at the top of the page adjacent to the homepage symbol is pulldown menu<br> labeled 'This Organism' with the following 4 display options for this page:<br> Overview :The top of page provides summary statistics for this genome including the numbers of subsystems, coding sequences, RNAs and other background information.<br> :A breakdown of the number of PEGs with hypothetical and non-hypothetical function assignments is provided in box in the top right corner of the page.<br> :Adjacent to the Taxonomy ID is the Wikipedia Globe that is linked to the Wikipedia entry for this organism. :On the bottom left of the page a bar graph depicts the percentages of PEGs for this genome that are present in at least one subsystem.<br> :Next to the bar graph a pie chart and accompanying expandable hierarchical tree, color coded to match the pie chart, organizes the subsystems<br> :present in this genome by cellular process. :At every level in the tree the number of PEGs in each category is listed in parentheses. :At the leaves of the tree are links to a Subsytem page in the SEED Viewer. Browse Genome :This display allows a you to walk the chromosome of the selected genome.<br> :If the genome is not completely assembled, the first contig will be selected. :The window size in terms of number of base pairs can be selected using the 'Window Size' pulldown menu, or the 'zoom in' or 'zoom out' buttons.<br> :The < and > buttons will move the window down or up the chromosome half the window size.<br> :The << and >> buttons will move the window down or up the chromosome a full window size.<br> :Under 'Options' you can select which features are displayed and the number of reading frames. By default the genome browser offers a two frame view of the currently selected organism.<br> :After selecting your options, click the 'Refresh' button to update the page. :On the middle line of the chromosome display you will see features not associated with a reading frame, such as rnas, pathogenicity islands or prophages.<br> :Hover over a feature in the chromosome display for a detailed description. :Clicking an item will take you to the Annotation page in the SEED Viewer for this feature. View Features View Reactions 28aa01c9cdbb22a396eea1c31f579690e3702dba 1545 1544 2006-11-03T16:55:31Z Mkubal 15 wikitext text/x-wiki Organism Page in SEED Viewer In the green bar at the top of the page adjacent to the homepage symbol is a pulldown menu<br> labeled 'This Organism' with the following 4 display options for this page:<br> Overview :The top of page provides summary statistics for this genome including the numbers of subsystems, coding sequences, RNAs and other background information.<br> :A breakdown of the number of PEGs with hypothetical and non-hypothetical function assignments is provided in box in the top right corner of the page.<br> :Adjacent to the Taxonomy ID is the Wikipedia Globe that is linked to the Wikipedia entry for this organism. :On the bottom left of the page a bar graph depicts the percentages of PEGs for this genome that are present in at least one subsystem.<br> :Next to the bar graph a pie chart and accompanying expandable hierarchical tree, color coded to match the pie chart, organizes the subsystems<br> :present in this genome by cellular process. :At every level in the tree the number of PEGs in each category is listed in parentheses. :At the leaves of the tree are links to a Subsytem page in the SEED Viewer. Browse Genome :This display allows a you to walk the chromosome of the selected genome.<br> :If the genome is not completely assembled, the first contig will be selected. :The window size in terms of number of base pairs can be selected using the 'Window Size' pulldown menu, or the 'zoom in' or 'zoom out' buttons.<br> :The < and > buttons will move the window down or up the chromosome half the window size.<br> :The << and >> buttons will move the window down or up the chromosome a full window size.<br> :Under 'Options' you can select which features are displayed and the number of reading frames. By default the genome browser offers a two frame view of the currently selected organism.<br> :After selecting your options, click the 'Refresh' button to update the page. :On the middle line of the chromosome display you will see features not associated with a reading frame, such as rnas, pathogenicity islands or prophages.<br> :Hover over a feature in the chromosome display for a detailed description. :Clicking an item will take you to the Annotation page in the SEED Viewer for this feature. View Features View Reactions a3a55f9b5f3b7e411bf862d0defc327c50623c30 1546 1545 2006-11-03T16:56:34Z Mkubal 15 wikitext text/x-wiki Organism Page in SEED Viewer In the green bar at the top of the page adjacent to the homepage symbol is a pulldown menu<br> labeled 'This Organism' with the following 4 display options for this page:<br> Overview :The top of page provides summary statistics for this genome including the numbers of subsystems, coding sequences, RNAs and other background information.<br> :A breakdown of the number of PEGs with hypothetical and non-hypothetical function assignments is provided in box in the top right corner of the page.<br> :Adjacent to the Taxonomy ID is the Wikipedia Globe that is linked to the Wikipedia entry for this organism. :On the bottom left of the page a bar graph depicts the percentages of PEGs for this genome that are present in at least one subsystem.<br> :Next to the bar graph a pie chart and accompanying expandable hierarchical tree, color coded to match the pie chart, organizes the subsystems<br> :present in this genome by cellular process. :At every level in the tree the number of PEGs in each category is listed in parentheses. :At the leaves of the tree are links to a Subsytem page in the SEED Viewer. Browse Genome :This display allows you to walk the chromosome of the selected genome.<br> :If the genome is not completely assembled, the first contig will be selected. :The window size in terms of number of base pairs can be selected using the 'Window Size' pulldown menu, or the 'zoom in' or 'zoom out' buttons.<br> :The < and > buttons will move the window down or up the chromosome half the window size.<br> :The << and >> buttons will move the window down or up the chromosome a full window size.<br> :Under 'Options' you can select which features are displayed and the number of reading frames. By default the genome browser offers a two frame view of the currently selected organism.<br> :After selecting your options, click the 'Refresh' button to update the page. :On the middle line of the chromosome display you will see features not associated with a reading frame, such as rnas, pathogenicity islands or prophages.<br> :Hover over a feature in the chromosome display for a detailed description. :Clicking an item will take you to the Annotation page in the SEED Viewer for this feature. View Features View Reactions b38a07ac64b62e779215b4197606dae9a0194211 1547 1546 2006-11-03T19:46:01Z Mkubal 15 wikitext text/x-wiki Organism Page in SEED Viewer In the green bar at the top of the page adjacent to the homepage symbol is a pulldown menu<br> labeled 'This Organism' with the following 4 display options for this page:<br> Overview :The top of page provides summary statistics for this genome including the numbers of subsystems, coding sequences, RNAs and other background information.<br> :A breakdown of the number of PEGs with hypothetical and non-hypothetical function assignments is provided in box in the top right corner of the page.<br> :Adjacent to the Taxonomy ID is the Wikipedia Globe that is linked to the Wikipedia entry for this organism. :On the bottom left of the page a bar graph depicts the percentages of PEGs for this genome that are present in at least one subsystem.<br> :Next to the bar graph a pie chart and accompanying expandable hierarchical tree, color coded to match the pie chart, organizes the subsystems<br> :present in this genome by cellular process. :At every level in the tree the number of PEGs in each category is listed in parentheses. :At the leaves of the tree are links to a Subsytem page in the SEED Viewer. Browse Genome :This display allows you to walk the chromosome of the selected genome.<br> :If the genome is not completely assembled, the first contig will be selected. :The window size in terms of number of base pairs can be selected using the 'Window Size' pulldown menu, or the 'zoom in' or 'zoom out' buttons.<br> :The < and > buttons will move the window down or up the chromosome half the window size.<br> :The << and >> buttons will move the window down or up the chromosome a full window size.<br> :Under 'Options' you can select which features are displayed and the number of reading frames. By default the genome browser offers a two frame view of the currently selected organism.<br> :After selecting your options, click the 'Refresh' button to update the page. :On the middle line of the chromosome display you will see features not associated with a reading frame, such as rnas, pathogenicity islands or prophages.<br> :Hover over a feature in the chromosome display for a detailed description. :Clicking an item will take you to the Annotation page in the SEED Viewer for this feature. View Features :Selecting this display provides a table containing feature ID, functional assignment, starting and stopping location in base pairs relative<br> to the beginning of the contig, feature type and a list of aliases.<br> :The total number of features for this genome is displayed above the table.<br> :Use the 'next>>' and 'last>>' links to quickly scroll through sets of 10 features.<br> :Filter features across the entire genome by using the text entry boxes in the 'Functional Assignment', 'Type' or 'Aliases' column header and then clicking enter. :Sort or reverse sort the tables using the triangle in the columns headers. :Export all or a subset of the features, after filtering, of a genome to a spreadsheet file using the 'Export Table' button. View Reactions 5ab656ea90a7a406752f5eebb29793b58eb05422 1548 1547 2006-11-03T19:47:47Z Mkubal 15 wikitext text/x-wiki Organism Page in SEED Viewer In the green bar at the top of the page adjacent to the homepage symbol is a pulldown menu<br> labeled 'This Organism' with the following 4 display options for this page:<br> Overview :The top of page provides summary statistics for this genome including the numbers of subsystems, coding sequences, RNAs and other background information.<br> :A breakdown of the number of PEGs with hypothetical and non-hypothetical function assignments is provided in box in the top right corner of the page.<br> :Adjacent to the Taxonomy ID is the Wikipedia Globe that is linked to the Wikipedia entry for this organism. :On the bottom left of the page a bar graph depicts the percentages of PEGs for this genome that are present in at least one subsystem.<br> :Next to the bar graph a pie chart and accompanying expandable hierarchical tree, color coded to match the pie chart, organizes the subsystems<br> :present in this genome by cellular process. :At every level in the tree the number of PEGs in each category is listed in parentheses. :At the leaves of the tree are links to a Subsytem page in the SEED Viewer. Browse Genome :This display allows you to walk the chromosome of the selected genome.<br> :If the genome is not completely assembled, the first contig will be selected. :The window size in terms of number of base pairs can be selected using the 'Window Size' pulldown menu, or the 'zoom in' or 'zoom out' buttons.<br> :The < and > buttons will move the window down or up the chromosome half the window size.<br> :The << and >> buttons will move the window down or up the chromosome a full window size.<br> :Under 'Options' you can select which features are displayed and the number of reading frames. By default the genome browser offers a two frame view of the currently selected organism.<br> :After selecting your options, click the 'Refresh' button to update the page. :On the middle line of the chromosome display you will see features not associated with a reading frame, such as rnas, pathogenicity islands or prophages.<br> :Hover over a feature in the chromosome display for a detailed description. :Clicking an item will take you to the Annotation page in the SEED Viewer for this feature. View Features :Selecting this display provides a table containing feature ID, functional assignment, starting and stopping location in base pairs relative<br> :to the beginning of the contig, feature type and a list of aliases.<br> :The total number of features for this genome is displayed above the table.<br> :Use the 'next>>' and 'last>>' links to quickly scroll through sets of 10 features.<br> :Filter features across the entire genome by using the text entry boxes in the 'Functional Assignment', 'Type' or 'Aliases' column header and then hitting enter. :Sort or reverse sort the tables using the triangle in the columns headers. :Export all or a subset of the features, after filtering, of a genome to a spreadsheet file using the 'Export Table' button. View Reactions cde73f5eb5d52d1ab0af372c7a2920358b271a25 1549 1548 2006-11-03T19:48:46Z Mkubal 15 wikitext text/x-wiki Organism Page in SEED Viewer In the green bar at the top of the page adjacent to the homepage symbol is a pulldown menu<br> labeled 'This Organism' with the following 4 display options for this page:<br> Overview :The top of page provides summary statistics for this genome including the numbers of subsystems, coding sequences, RNAs and other background information.<br> :A breakdown of the number of PEGs with hypothetical and non-hypothetical function assignments is provided in box in the top right corner of the page.<br> :Adjacent to the Taxonomy ID is the Wikipedia Globe that is linked to the Wikipedia entry for this organism. :On the bottom left of the page a bar graph depicts the percentages of PEGs for this genome that are present in at least one subsystem.<br> :Next to the bar graph a pie chart and accompanying expandable hierarchical tree, color coded to match the pie chart, organizes the subsystems<br> :present in this genome by cellular process. :At every level in the tree the number of PEGs in each category is listed in parentheses. :At the leaves of the tree are links to a Subsytem page in the SEED Viewer. Browse Genome :This display allows you to walk the chromosome of the selected genome.<br> :If the genome is not completely assembled, the first contig will be selected. :The window size in terms of number of base pairs can be selected using the 'Window Size' pulldown menu, or the 'zoom in' or 'zoom out' buttons.<br> :The < and > buttons will move the window down or up the chromosome half the window size.<br> :The << and >> buttons will move the window down or up the chromosome a full window size.<br> :Under 'Options' you can select which features are displayed and the number of reading frames. By default the genome browser offers a two frame view of the currently selected organism.<br> :After selecting your options, click the 'Refresh' button to update the page. :On the middle line of the chromosome display you will see features not associated with a reading frame, such as rnas, pathogenicity islands or prophages.<br> :Hover over a feature in the chromosome display for a detailed description. :Clicking an item will take you to the Annotation page in the SEED Viewer for this feature. View Features :Selecting this display provides a table containing feature ID, functional assignment, starting and stopping location in terms of base pairs relative<br> :to the beginning of the contig, feature type and a list of aliases.<br> :The total number of features for this genome is displayed above the table.<br> :Use the 'next>>' and 'last>>' links to quickly scroll through sets of 10 features.<br> :Filter features across the entire genome by using the text entry boxes in the 'Functional Assignment', 'Type' or 'Aliases' column header and then hitting enter. :Sort or reverse sort the tables using the triangle in the columns headers. :Export all or a subset of the features, after filtering, of a genome to a spreadsheet file using the 'Export Table' button. View Reactions 59f8d6e0534a4e33df37604e7a739bbf23f46c53 0 1387 1550 2006-11-03T20:44:31Z Mkubal 15 wikitext text/x-wiki SEED Viewer Annotation Page Overview :This page offers access to the data relating to a feature. By default the Overview version of the page <br> :is initially displayed providing the feature's function assignment, source organism, the role it performs<br> :in a subsystem, and a graphic displaying it's genomic context. :In the graphic each line represents a different genome. The genome of the feature that is the subject of this page<br> :is on the first line with the subject feature in red and centered in a 16kb window. Features on the same line that have<br> :a gray shadow are functionally coupled to the subject feature. Features in different genome that share the same color or <br> :number are similar. Clicking 'Diverse Genomes' will change the genomes in the graphic to a set that is more phylogentically<br> :distant to the subject feature's genome. Sequence Data :From the green bar at the top of page, selecting the 'This Protein' menu will give the user the choice of viewing the<br> this feature's DNA sequence, DNA with flanking sequence or amino acid sequence. Tools :From the green bar at the top of the page, selecting the 'Tools' menu will give the user the choice of the following tools<br> :to analyze this feature:<br> ::TMpred :TMHMM :Gram negative PSORT :Gram negative SignalP :Gram positive PSORT :Gram positive SignalP :LipoP :InterProScan :Radar :PPSearch :Gram negative CELLO :Gram positive CELLO :ProDom Literature 4a5d4c9808a04887cac770d2cb34d03bab9d5614 0 1388 1552 2006-11-03T20:46:58Z Mkubal 15 wikitext text/x-wiki SEED Viewer Annotation Page Overview :This page offers access to the data relating to a feature. By default the Overview version of the page <br> :is initially displayed providing the feature's function assignment, source organism, the role it performs<br> :in a subsystem, and a graphic displaying it's genomic context. :In the graphic each line represents a different genome. The genome of the feature that is the subject of this page<br> :is on the first line with the subject feature in red and centered in a 16kb window. Features on the same line that have<br> :a gray shadow are functionally coupled to the subject feature. Features in different genome that share the same color or <br> :number are similar. Clicking 'Diverse Genomes' will change the genomes in the graphic to a set that is more phylogentically<br> :distant to the subject feature's genome. Sequence Data :From the green bar at the top of page, selecting the 'This Protein' menu will give the user the choice of viewing the<br> this feature's DNA sequence, DNA with flanking sequence or amino acid sequence. Tools :From the green bar at the top of the page, selecting the 'Tools' menu will give the user the choice of the following tools<br> :to analyze this feature:<br> ::TMpred :TMHMM :Gram negative PSORT :Gram negative SignalP :Gram positive PSORT :Gram positive SignalP :LipoP :InterProScan :Radar :PPSearch :Gram negative CELLO :Gram positive CELLO :ProDom Literature 4a5d4c9808a04887cac770d2cb34d03bab9d5614 1553 1552 2006-11-03T20:48:40Z Mkubal 15 wikitext text/x-wiki SEED Viewer Annotation Page Overview :This page offers access to the data relating to a feature. By default the Overview version of the page <br> :is initially displayed providing the feature's function assignment, source organism, the role it performs<br> :in a subsystem, and a graphic displaying it's genomic context. :In the graphic each line represents a different genome. The genome of the feature that is the subject of this page<br> :is on the first line with the subject feature in red and centered in a 16kb window. Features on the same line that have<br> :a gray shadow are functionally coupled to the subject feature. Features in different genome that share the same color or <br> :number are similar. Clicking 'Diverse Genomes' will change the genomes in the graphic to a set that is more phylogentically<br> :distant to the subject feature's genome. Sequence Data :From the green bar at the top of page, selecting the 'This Protein' menu will give the user the choice of viewing the<br> this feature's DNA sequence, DNA with flanking sequence or amino acid sequence. Tools :From the green bar at the top of the page, selecting the 'Tools' menu will give the user the choice of the following tools<br> :to analyze this feature:<br> ::TMpred ::TMHMM ::Gram negative PSORT ::Gram negative SignalP ::Gram positive PSORT ::Gram positive SignalP ::LipoP ::InterProScan ::Radar ::PPSearch ::Gram negative CELLO ::Gram positive CELLO ::ProDom Literature da2e66356106a53255c08232dab1c831cb1386db 1554 1553 2006-11-03T20:51:06Z Mkubal 15 wikitext text/x-wiki SEED Viewer Annotation Page Overview :This page offers access to the data relating to a feature. By default the Overview version of the page <br> :is initially displayed providing the feature's function assignment, source organism, the role it performs<br> :in a subsystem, and a graphic displaying it's genomic context. :In the graphic each line represents a different genome. The genome of the feature that is the subject of this page<br> :is on the first line with the subject feature in red and centered in a 16kb window. Features on the same line that have<br> :a gray shadow are functionally coupled to the subject feature. Features in different genome that share the same color or <br> :number are similar. Clicking 'Diverse Genomes' will change the genomes in the graphic to a set that is more phylogentically<br> :distant to the subject feature's genome. Sequence Data :From the green bar at the top of page, selecting the 'This Protein' menu will give the user the choice of viewing the<br> :this feature's DNA sequence, DNA with flanking sequence or amino acid sequence. Tools :From the green bar at the top of the page, selecting the 'Tools' menu will give the user the choice of the following tools<br> :to analyze this feature:<br> ::TMpred ::TMHMM ::Gram negative PSORT ::Gram negative SignalP ::Gram positive PSORT ::Gram positive SignalP ::LipoP ::InterProScan ::Radar ::PPSearch ::Gram negative CELLO ::Gram positive CELLO ::ProDom Literature 07f329b422f8995f23aa889ee124179e1889ab01 0 1389 1555 2006-11-03T21:03:41Z Mkubal 15 wikitext text/x-wiki SEED Viewer Functional Role Page In the top right corner of this page are statistics on the number of PEGs within the SEED database that currently are<br> associated with this functional role and within how many different organisms these PEGs are present. f52b004fb8fa9faa4a408b56400aae7a46ff062e 0 1390 1556 2006-11-03T21:08:00Z Mkubal 15 wikitext text/x-wiki SEED Viewer Subsystem Page Overview :Statistics :Functional Roles Table Populated Subsystem Notes 8341b78ef27a5d29b565d20ae366ec3667ee755d 1557 1556 2006-11-07T17:03:36Z Mkubal 15 wikitext text/x-wiki SEED Viewer Subsystem Page Overview :On the top, right of the page a box contains the statistics for this subsystem including the<br> :number of functional roles, total number of genomes, and the number of genomes where this subsystem<br> :is present,not present or is still a work in progress. :The username of annotator who is responsible for the subsystem is listed. Diagram :The noninteractive diagram illustrates the connectivity of the roles, alternate pathways, intermediate compounds and cofactors. :The functional role abbreviations in the boxes reference the roles in the table below. Currently diagrams are not present for every subsystem. Functional Roles Table :This list all the functional roles that define the subsystem. Each functional role is linked to a Functional Role page in the SEED Viewer.<br> :When present the entry in the EC column links to KEGG. :In the Ontologies column, the buttons 'Rc' and 'GO' are shaded green if a KEGG reaction<br> :or GO ontology term respectively is associated with this functional role. The 'Rc' button is linked to back to the Functional Role page<br> :which displays the KEGG reaction id. The 'GO' button is linked to an entry in AmiGO. :Functional roles that share the same abbreviation in the Group Alias column have been grouped together by the annotator, usually because<br> they share a similar function but are found in different organisms. These groupings can be utilized in visualizing the Populated Subsystem table. Populated Subsystem : Notes 45281cb85bc0d383827236bb409830e8ee70ff47 1558 1557 2006-11-07T17:15:41Z Mkubal 15 wikitext text/x-wiki SEED Viewer Subsystem Page Overview :On the top, right of the page a box contains the statistics for this subsystem including the<br> :number of functional roles, total number of genomes, and the number of genomes where this subsystem<br> :is present,not present or is still a work in progress. :The username of annotator who is responsible for the subsystem is listed. Diagram :The noninteractive diagram illustrates the connectivity of the roles, alternate pathways, intermediate compounds and cofactors. :The functional role abbreviations in the boxes reference the roles in the table below. Currently diagrams are not present for every subsystem. Functional Roles Table :This list all the functional roles that define the subsystem. Each functional role is linked to a Functional Role page in the SEED Viewer.<br> :When present the entry in the EC column links to KEGG. :In the Ontologies column, the buttons 'Rc' and 'GO' are shaded green if a KEGG reaction<br> :or GO ontology term respectively is associated with this functional role. The 'Rc' button is linked to back to the Functional Role page<br> :which displays the KEGG reaction id. The 'GO' button is linked to an entry in AmiGO. :Functional roles that share the same abbreviation in the Group Alias column have been grouped together by the annotator, usually because<br> :they share a similar function but are found in different organisms. These groupings can be utilized in visualizing the Populated Subsystem table.<br> :If the annotator of the subsytem has defined subsets of functional roles, the 'Highlight subsets' menu will be present above the table. Use this menu<br> :to highlight defined internal pathways of the subsystem in within the table.<br> Populated Subsystem : Notes 7b444763ea55d5a16493ecd2515fc5dc12fbe73e 1559 1558 2006-11-07T17:49:56Z Mkubal 15 wikitext text/x-wiki SEED Viewer Subsystem Page Overview :On the top, right of the page a box contains the statistics for this subsystem including the<br> :number of functional roles, total number of genomes, and the number of genomes where this subsystem<br> :is present,not present or is still a work in progress. :The username of annotator who is responsible for the subsystem is listed. Diagram :The noninteractive diagram illustrates the connectivity of the roles, alternate pathways, intermediate compounds and cofactors. :The functional role abbreviations in the boxes reference the roles in the table below. Currently diagrams are not present for every subsystem. Functional Roles Table :This list all the functional roles that define the subsystem. Each functional role is linked to a Functional Role page in the SEED Viewer.<br> :When present the entry in the EC column links to KEGG. :In the Ontologies column, the buttons 'Rc' and 'GO' are shaded green if a KEGG reaction<br> :or GO ontology term respectively is associated with this functional role. The 'Rc' button is linked to back to the Functional Role page<br> :which displays the KEGG reaction id. The 'GO' button is linked to an entry in AmiGO. :Functional roles that share the same abbreviation in the Group Alias column have been grouped together by the annotator, usually because<br> :they share a similar function but are found in different organisms. These groupings can be utilized in visualizing the Populated Subsystem table.<br> :If the annotator of the subsytem has defined subsets of functional roles, the 'Highlight subsets' menu will be present above the table. Use this menu<br> :to highlight the roles in the table that define internal pathways of the subsystem.<br> Populated Subsystem :By default this spreadsheet shows only genomes that possess a functional variant of this subsystem.<br> :By checking the box 'Show organisms classified as not present in this subsystem' or 'Show organisms classified as work in progress'<br> :and clicking the 'Refresh populated subsystem' button, the spreadsheet will be updated with these genomes.<br> :Use the 'Limit genomes by taxonomy' menu, followed by the refresh button to limit the table to a specific group of organisms<br>. ::Hovering over any element in a cell will display the SEEED ID(s) of the gene(s) it contains .<br> :Spreadsheet cells in the same row that contain rectangles of the same color represent genes that are clustered.<br> :A colored rectangle with an adjacent triangle indicate multiple genes are associated with this role.<br> :A white rectangle with a number indicates an unclustered gene(s) is associated with this role. The number indicates the number of genes<br>. :A black triangle indicates that there are more than five clusters of genes present in this genome for this subsystem. Notes 0ade5137dc76e753dfe5a7a04df9d60905d33013 1560 1559 2006-11-07T17:50:19Z Mkubal 15 wikitext text/x-wiki SEED Viewer Subsystem Page Overview :On the top, right of the page a box contains the statistics for this subsystem including the<br> :number of functional roles, total number of genomes, and the number of genomes where this subsystem<br> :is present,not present or is still a work in progress. :The username of annotator who is responsible for the subsystem is listed. Diagram :The noninteractive diagram illustrates the connectivity of the roles, alternate pathways, intermediate compounds and cofactors. :The functional role abbreviations in the boxes reference the roles in the table below. Currently diagrams are not present for every subsystem. Functional Roles Table :This list all the functional roles that define the subsystem. Each functional role is linked to a Functional Role page in the SEED Viewer.<br> :When present the entry in the EC column links to KEGG. :In the Ontologies column, the buttons 'Rc' and 'GO' are shaded green if a KEGG reaction<br> :or GO ontology term respectively is associated with this functional role. The 'Rc' button is linked to back to the Functional Role page<br> :which displays the KEGG reaction id. The 'GO' button is linked to an entry in AmiGO. :Functional roles that share the same abbreviation in the Group Alias column have been grouped together by the annotator, usually because<br> :they share a similar function but are found in different organisms. These groupings can be utilized in visualizing the Populated Subsystem table.<br> :If the annotator of the subsytem has defined subsets of functional roles, the 'Highlight subsets' menu will be present above the table. Use this menu<br> :to highlight the roles in the table that define internal pathways of the subsystem.<br> Populated Subsystem :By default this spreadsheet shows only genomes that possess a functional variant of this subsystem.<br> :By checking the box 'Show organisms classified as not present in this subsystem' or 'Show organisms classified as work in progress'<br> :and clicking the 'Refresh populated subsystem' button, the spreadsheet will be updated with these genomes.<br> :Use the 'Limit genomes by taxonomy' menu, followed by the refresh button to limit the table to a specific group of organisms<br>. :Hovering over any element in a cell will display the SEEED ID(s) of the gene(s) it contains .<br> :Spreadsheet cells in the same row that contain rectangles of the same color represent genes that are clustered.<br> :A colored rectangle with an adjacent triangle indicate multiple genes are associated with this role.<br> :A white rectangle with a number indicates an unclustered gene(s) is associated with this role. The number indicates the number of genes<br>. :A black triangle indicates that there are more than five clusters of genes present in this genome for this subsystem. Notes 627922c0b2e49522d3a4f4b19601f61b79c01bdc 1561 1560 2006-11-07T17:50:46Z Mkubal 15 wikitext text/x-wiki SEED Viewer Subsystem Page Overview :On the top, right of the page a box contains the statistics for this subsystem including the<br> :number of functional roles, total number of genomes, and the number of genomes where this subsystem<br> :is present,not present or is still a work in progress. :The username of annotator who is responsible for the subsystem is listed. Diagram :The noninteractive diagram illustrates the connectivity of the roles, alternate pathways, intermediate compounds and cofactors. :The functional role abbreviations in the boxes reference the roles in the table below. Currently diagrams are not present for every subsystem. Functional Roles Table :This list all the functional roles that define the subsystem. Each functional role is linked to a Functional Role page in the SEED Viewer.<br> :When present the entry in the EC column links to KEGG. :In the Ontologies column, the buttons 'Rc' and 'GO' are shaded green if a KEGG reaction<br> :or GO ontology term respectively is associated with this functional role. The 'Rc' button is linked to back to the Functional Role page<br> :which displays the KEGG reaction id. The 'GO' button is linked to an entry in AmiGO. :Functional roles that share the same abbreviation in the Group Alias column have been grouped together by the annotator, usually because<br> :they share a similar function but are found in different organisms. These groupings can be utilized in visualizing the Populated Subsystem table.<br> :If the annotator of the subsytem has defined subsets of functional roles, the 'Highlight subsets' menu will be present above the table. Use this menu<br> :to highlight the roles in the table that define internal pathways of the subsystem.<br> Populated Subsystem :By default this spreadsheet shows only genomes that possess a functional variant of this subsystem.<br> :By checking the box 'Show organisms classified as not present in this subsystem' or 'Show organisms classified as work in progress'<br> :and clicking the 'Refresh populated subsystem' button, the spreadsheet will be updated with these genomes.<br> :Use the 'Limit genomes by taxonomy' menu, followed by the refresh button to limit the table to a specific group of organisms.<br> :Hovering over any element in a cell will display the SEEED ID(s) of the gene(s) it contains .<br> :Spreadsheet cells in the same row that contain rectangles of the same color represent genes that are clustered.<br> :A colored rectangle with an adjacent triangle indicate multiple genes are associated with this role.<br> :A white rectangle with a number indicates an unclustered gene(s) is associated with this role. The number indicates the number of genes<br>. :A black triangle indicates that there are more than five clusters of genes present in this genome for this subsystem. Notes 10f79f406934862bbc8e2821f4bc20d6f67649bd 1562 1561 2006-11-07T17:51:23Z Mkubal 15 wikitext text/x-wiki SEED Viewer Subsystem Page Overview :On the top, right of the page a box contains the statistics for this subsystem including the<br> :number of functional roles, total number of genomes, and the number of genomes where this subsystem<br> :is present,not present or is still a work in progress. :The username of annotator who is responsible for the subsystem is listed. Diagram :The noninteractive diagram illustrates the connectivity of the roles, alternate pathways, intermediate compounds and cofactors. :The functional role abbreviations in the boxes reference the roles in the table below. Currently diagrams are not present for every subsystem. Functional Roles Table :This list all the functional roles that define the subsystem. Each functional role is linked to a Functional Role page in the SEED Viewer.<br> :When present the entry in the EC column links to KEGG. :In the Ontologies column, the buttons 'Rc' and 'GO' are shaded green if a KEGG reaction<br> :or GO ontology term respectively is associated with this functional role. The 'Rc' button is linked to back to the Functional Role page<br> :which displays the KEGG reaction id. The 'GO' button is linked to an entry in AmiGO. :Functional roles that share the same abbreviation in the Group Alias column have been grouped together by the annotator, usually because<br> :they share a similar function but are found in different organisms. These groupings can be utilized in visualizing the Populated Subsystem table.<br> :If the annotator of the subsytem has defined subsets of functional roles, the 'Highlight subsets' menu will be present above the table. Use this menu<br> :to highlight the roles in the table that define internal pathways of the subsystem.<br> Populated Subsystem :By default this spreadsheet shows only genomes that possess a functional variant of this subsystem.<br> :By checking the box 'Show organisms classified as not present in this subsystem' or 'Show organisms classified as work in progress'<br> :and clicking the 'Refresh populated subsystem' button, the spreadsheet will be updated with these genomes.<br> :Use the 'Limit genomes by taxonomy' menu, followed by the refresh button to limit the table to a specific group of organisms.<br> :Hovering over any element in a cell will display the SEEED ID(s) of the gene(s) it contains .<br> :Spreadsheet cells in the same row that contain rectangles of the same color represent genes that are clustered.<br> :A colored rectangle with an adjacent triangle indicate multiple genes are associated with this role.<br> :A white rectangle with a number indicates an unclustered gene(s) is associated with this role. The number indicates the number of genes.<br> :A black triangle indicates that there are more than five clusters of genes present in this genome for this subsystem<br>. Notes 4a61138a358d3ff3554567c42e14dc0ab14e0796 1563 1562 2006-11-07T17:51:46Z Mkubal 15 wikitext text/x-wiki SEED Viewer Subsystem Page Overview :On the top, right of the page a box contains the statistics for this subsystem including the<br> :number of functional roles, total number of genomes, and the number of genomes where this subsystem<br> :is present,not present or is still a work in progress. :The username of annotator who is responsible for the subsystem is listed. Diagram :The noninteractive diagram illustrates the connectivity of the roles, alternate pathways, intermediate compounds and cofactors. :The functional role abbreviations in the boxes reference the roles in the table below. Currently diagrams are not present for every subsystem. Functional Roles Table :This list all the functional roles that define the subsystem. Each functional role is linked to a Functional Role page in the SEED Viewer.<br> :When present the entry in the EC column links to KEGG. :In the Ontologies column, the buttons 'Rc' and 'GO' are shaded green if a KEGG reaction<br> :or GO ontology term respectively is associated with this functional role. The 'Rc' button is linked to back to the Functional Role page<br> :which displays the KEGG reaction id. The 'GO' button is linked to an entry in AmiGO. :Functional roles that share the same abbreviation in the Group Alias column have been grouped together by the annotator, usually because<br> :they share a similar function but are found in different organisms. These groupings can be utilized in visualizing the Populated Subsystem table.<br> :If the annotator of the subsytem has defined subsets of functional roles, the 'Highlight subsets' menu will be present above the table. Use this menu<br> :to highlight the roles in the table that define internal pathways of the subsystem.<br> Populated Subsystem :By default this spreadsheet shows only genomes that possess a functional variant of this subsystem.<br> :By checking the box 'Show organisms classified as not present in this subsystem' or 'Show organisms classified as work in progress'<br> :and clicking the 'Refresh populated subsystem' button, the spreadsheet will be updated with these genomes.<br> :Use the 'Limit genomes by taxonomy' menu, followed by the refresh button to limit the table to a specific group of organisms.<br> :Hovering over any element in a cell will display the SEEED ID(s) of the gene(s) it contains .<br> :Spreadsheet cells in the same row that contain rectangles of the same color represent genes that are clustered.<br> :A colored rectangle with an adjacent triangle indicate multiple genes are associated with this role.<br> :A white rectangle with a number indicates an unclustered gene(s) is associated with this role. The number indicates the number of genes.<br> :A black triangle indicates that there are more than five clusters of genes present in this genome for this subsystem.<br> Notes 8fe38453dee590b0db4a848d2947dad5bedc7ced 1564 1563 2006-11-07T18:40:31Z Mkubal 15 wikitext text/x-wiki SEED Viewer Subsystem Page Overview :On the top, right of the page a box contains the statistics for this subsystem including the<br> :number of functional roles, total number of genomes, and the number of genomes where this subsystem<br> :is present,not present or is still a work in progress. :The username of annotator who is responsible for the subsystem is listed. Diagram :The noninteractive diagram illustrates the connectivity of the roles, alternate pathways, intermediate compounds and cofactors. :The functional role abbreviations in the boxes reference the roles in the table below. Currently diagrams are not present for every subsystem. Functional Roles Table :This list all the functional roles that define the subsystem. Each functional role is linked to a Functional Role page in the SEED Viewer.<br> :When present the entry in the EC column links to KEGG. :In the Ontologies column, the buttons 'Rc' and 'GO' are shaded green if a KEGG reaction<br> :or GO ontology term respectively is associated with this functional role. The 'Rc' button is linked to back to the Functional Role page<br> :which displays the KEGG reaction id. The 'GO' button is linked to an entry in AmiGO. :Functional roles that share the same abbreviation in the Group Alias column have been grouped together by the annotator, usually because<br> :they share a similar function but are found in different organisms. These groupings can be utilized in visualizing the Populated Subsystem table.<br> :If the annotator of the subsytem has defined subsets of functional roles, the 'Highlight subsets' menu will be present above the table. Use this menu<br> :to highlight the roles in the table that define internal pathways of the subsystem.<br> Populated Subsystem :By default this spreadsheet shows only genomes that possess a functional variant of this subsystem.<br> :An explanation of number in the Variant column is found by selecting 'View Notes' under the 'This Subsystem' menu in the green bar at the top of the page. :At the bottom of the page, checking the box 'Show organisms classified as not present in this subsystem' or 'Show organisms classified as work in progress'<br> :and clicking the 'Refresh populated subsystem' button, will update the spreadsheet with these genomes.<br> :Use the 'Limit genomes by taxonomy' menu, followed by the refresh button to limit the table to a specific group of organisms.<br> :Hovering over any element in a cell will display the SEEED ID(s) of the gene(s) it contains .<br> :Spreadsheet cells in the same row that contain rectangles of the same color represent genes that are clustered.<br> :A colored rectangle with an adjacent triangle indicate multiple genes are associated with this role.<br> :A white rectangle with a number indicates an unclustered gene(s) is associated with this role. The number indicates the number of genes.<br> :A black triangle indicates that there are more than five clusters of genes present in this genome for this subsystem.<br> Notes e3434049cc87797823f769c0ec91e330387b92c7 0 1390 1565 1564 2006-11-07T18:50:50Z Mkubal 15 wikitext text/x-wiki SEED Viewer Subsystem Page Use the 'This Subsystem' menu in the green bar at the top of the page to view the Populated Subsystem spreadsheet or to 'View Notes' for this susbystem.<br> or return to the 'Overview'. Overview :On the top, right of the page a box contains the statistics for this subsystem including the<br> :number of functional roles, total number of genomes, and the number of genomes where this subsystem<br> :is present,not present or is still a work in progress. :The username of annotator who is responsible for the subsystem is listed. Diagram :The noninteractive diagram illustrates the connectivity of the roles, alternate pathways, intermediate compounds and cofactors. :The functional role abbreviations in the boxes reference the roles in the table below. Currently diagrams are not present for every subsystem. Functional Roles Table :This list all the functional roles that define the subsystem. Each functional role is linked to a Functional Role page in the SEED Viewer.<br> :When present the entry in the EC column links to KEGG. :In the Ontologies column, the buttons 'Rc' and 'GO' are shaded green if a KEGG reaction<br> :or GO ontology term respectively is associated with this functional role. The 'Rc' button is linked to back to the Functional Role page<br> :which displays the KEGG reaction id. The 'GO' button is linked to an entry in AmiGO. :Functional roles that share the same abbreviation in the Group Alias column have been grouped together by the annotator, usually because<br> :they share a similar function but are found in different organisms. These groupings can be utilized in visualizing the Populated Subsystem table.<br> :If the annotator of the subsytem has defined subsets of functional roles, the 'Highlight subsets' menu will be present above the table. Use this menu<br> :to highlight the roles in the table that define internal pathways of the subsystem.<br> Populated Subsystem :By default this spreadsheet shows only genomes that possess a functional variant of this subsystem.<br> :An explanation of number in the Variant column is found by selecting 'View Notes' under the 'This Subsystem' menu in the green bar at the top of the page. :At the bottom of the page, checking the box 'Show organisms classified as not present in this subsystem' or 'Show organisms classified as work in progress'<br> :and clicking the 'Refresh populated subsystem' button, will update the spreadsheet with these genomes.<br> :Use the 'Limit genomes by taxonomy' menu, followed by the refresh button to limit the table to a specific group of organisms.<br> :Use the 'Collapse/Expand Group Aliases' button to combine or separate columns that are in the same group.(not yet implemented.Br> :Hovering over any element in a cell will display the SEED ID(s) of the gene(s) it contains .<br> :Spreadsheet cells in the same row that contain rectangles of the same color represent genes that are clustered.<br> :A colored rectangle with an adjacent triangle indicate multiple genes are associated with this role.<br> :A white rectangle with a number indicates an unclustered gene(s) is associated with this role. The number indicates the number of genes.<br> :A black triangle indicates that there are more than five clusters of genes present in this genome for this subsystem.<br> Notes :The notes page contains explanations of the variant codes, references and additional information about this subsystem. d74c81b45a74ffeb9814a38f57a64f368c4ded9f 1566 1565 2006-11-07T18:51:21Z Mkubal 15 wikitext text/x-wiki SEED Viewer Subsystem Page Use the 'This Subsystem' menu in the green bar at the top of the page to view the 'Populated Subsystem' spreadsheet or to 'View Notes' for this susbystem.<br> or to return to the 'Overview'. Overview :On the top, right of the page a box contains the statistics for this subsystem including the<br> :number of functional roles, total number of genomes, and the number of genomes where this subsystem<br> :is present,not present or is still a work in progress. :The username of annotator who is responsible for the subsystem is listed. Diagram :The noninteractive diagram illustrates the connectivity of the roles, alternate pathways, intermediate compounds and cofactors. :The functional role abbreviations in the boxes reference the roles in the table below. Currently diagrams are not present for every subsystem. Functional Roles Table :This list all the functional roles that define the subsystem. Each functional role is linked to a Functional Role page in the SEED Viewer.<br> :When present the entry in the EC column links to KEGG. :In the Ontologies column, the buttons 'Rc' and 'GO' are shaded green if a KEGG reaction<br> :or GO ontology term respectively is associated with this functional role. The 'Rc' button is linked to back to the Functional Role page<br> :which displays the KEGG reaction id. The 'GO' button is linked to an entry in AmiGO. :Functional roles that share the same abbreviation in the Group Alias column have been grouped together by the annotator, usually because<br> :they share a similar function but are found in different organisms. These groupings can be utilized in visualizing the Populated Subsystem table.<br> :If the annotator of the subsytem has defined subsets of functional roles, the 'Highlight subsets' menu will be present above the table. Use this menu<br> :to highlight the roles in the table that define internal pathways of the subsystem.<br> Populated Subsystem :By default this spreadsheet shows only genomes that possess a functional variant of this subsystem.<br> :An explanation of number in the Variant column is found by selecting 'View Notes' under the 'This Subsystem' menu in the green bar at the top of the page. :At the bottom of the page, checking the box 'Show organisms classified as not present in this subsystem' or 'Show organisms classified as work in progress'<br> :and clicking the 'Refresh populated subsystem' button, will update the spreadsheet with these genomes.<br> :Use the 'Limit genomes by taxonomy' menu, followed by the refresh button to limit the table to a specific group of organisms.<br> :Use the 'Collapse/Expand Group Aliases' button to combine or separate columns that are in the same group.(not yet implemented.Br> :Hovering over any element in a cell will display the SEED ID(s) of the gene(s) it contains .<br> :Spreadsheet cells in the same row that contain rectangles of the same color represent genes that are clustered.<br> :A colored rectangle with an adjacent triangle indicate multiple genes are associated with this role.<br> :A white rectangle with a number indicates an unclustered gene(s) is associated with this role. The number indicates the number of genes.<br> :A black triangle indicates that there are more than five clusters of genes present in this genome for this subsystem.<br> Notes :The notes page contains explanations of the variant codes, references and additional information about this subsystem. fd615a013b908f8f9cf4dcc9ffe22d4d247fe1c7 1567 1566 2006-11-07T18:52:18Z Mkubal 15 wikitext text/x-wiki SEED Viewer Subsystem Page Use the 'This Subsystem' menu in the green bar at the top of the page to view the 'Populated Subsystem' spreadsheet or to 'View Notes' for this susbystem.<br> or to return to the 'Overview'. Overview :On the top, right of the page a box contains the statistics for this subsystem including the<br> :number of functional roles, total number of genomes, and the number of genomes where this subsystem<br> :is present,not present or is still a work in progress. :The username of annotator who is responsible for the subsystem is listed. Diagram :The diagram illustrates the connectivity of the roles, alternate pathways, intermediate compounds and cofactors. :The functional role abbreviations in the boxes reference the roles in the table below. Currently diagrams are not present for every subsystem. Functional Roles Table :This list all the functional roles that define the subsystem. Each functional role is linked to a Functional Role page in the SEED Viewer.<br> :When present the entry in the EC column links to KEGG. :In the Ontologies column, the buttons 'Rc' and 'GO' are shaded green if a KEGG reaction<br> :or GO ontology term respectively is associated with this functional role. The 'Rc' button is linked to back to the Functional Role page<br> :which displays the KEGG reaction id. The 'GO' button is linked to an entry in AmiGO. :Functional roles that share the same abbreviation in the Group Alias column have been grouped together by the annotator, usually because<br> :they share a similar function but are found in different organisms. These groupings can be utilized in visualizing the Populated Subsystem table.<br> :If the annotator of the subsytem has defined subsets of functional roles, the 'Highlight subsets' menu will be present above the table. Use this menu<br> :to highlight the roles in the table that define internal pathways of the subsystem.<br> Populated Subsystem :By default this spreadsheet shows only genomes that possess a functional variant of this subsystem.<br> :An explanation of number in the Variant column is found by selecting 'View Notes' under the 'This Subsystem' menu in the green bar at the top of the page. :At the bottom of the page, checking the box 'Show organisms classified as not present in this subsystem' or 'Show organisms classified as work in progress'<br> :and clicking the 'Refresh populated subsystem' button, will update the spreadsheet with these genomes.<br> :Use the 'Limit genomes by taxonomy' menu, followed by the refresh button to limit the table to a specific group of organisms.<br> :Use the 'Collapse/Expand Group Aliases' button to combine or separate columns that are in the same group.(not yet implemented.Br> :Hovering over any element in a cell will display the SEED ID(s) of the gene(s) it contains .<br> :Spreadsheet cells in the same row that contain rectangles of the same color represent genes that are clustered.<br> :A colored rectangle with an adjacent triangle indicate multiple genes are associated with this role.<br> :A white rectangle with a number indicates an unclustered gene(s) is associated with this role. The number indicates the number of genes.<br> :A black triangle indicates that there are more than five clusters of genes present in this genome for this subsystem.<br> Notes :The notes page contains explanations of the variant codes, references and additional information about this subsystem. 2e841eac1439abee0c08dabb2cfbf9a67d579481 1568 1567 2006-11-07T18:54:42Z Mkubal 15 wikitext text/x-wiki SEED Viewer Subsystem Page Use the 'This Subsystem' menu in the green bar at the top of the page to view the 'Populated Subsystem' spreadsheet or to 'View Notes' for this susbystem.<br> or to return to the 'Overview'. Overview :On the top, right of the page a box contains the statistics for this subsystem including the<br> :number of functional roles, total number of genomes, and the number of genomes where this subsystem<br> :is present,not present or is still a work in progress. :The username of annotator who is responsible for the subsystem is listed. Diagram :The diagram illustrates the connectivity of the roles, alternate pathways, intermediate compounds and cofactors. :The functional role abbreviations in the boxes reference the roles in the table below. Currently diagrams are not present for every subsystem. Functional Roles Table :This list all the functional roles that define the subsystem. Each functional role is linked to a Functional Role page in the SEED Viewer.<br> :When present the entry in the EC column links to KEGG. :In the Ontologies column, the buttons 'Rc' and 'GO' are shaded green if a KEGG reaction<br> :or GO ontology term respectively is associated with this functional role. The 'Rc' button is linked to back to the Functional Role page<br> :which displays the KEGG reaction id. The 'GO' button is linked to an entry in AmiGO. :Functional roles that share the same abbreviation in the Group Alias column have been grouped together by the annotator, usually because<br> :they share a similar function but are found in different organisms. These groupings can be utilized in visualizing the Populated Subsystem table.<br> :If the annotator of the subsytem has defined subsets of functional roles, the 'Highlight subsets' menu will be present above the table. Use this menu<br> :to highlight the roles in the table that define internal pathways of the subsystem.<br> Populated Subsystem :By default this spreadsheet shows only genomes that possess a functional variant of this subsystem.<br> :An explanation of number in the Variant column is found by selecting 'View Notes' under the 'This Subsystem' menu in the green bar at the top of the page. :At the bottom of the page, checking the box 'Show organisms classified as not present in this subsystem' or 'Show organisms classified as work in progress' and clicking the 'Refresh populated subsystem' button, will update the spreadsheet with these genomes.<br> :Use the 'Limit genomes by taxonomy' menu, followed by the refresh button to limit the table to a specific group of organisms.<br> :Use the 'Collapse/Expand Group Aliases' button to combine or separate columns that are in the same group.(not yet implemented.Br> :Hovering over any element in a cell will display the SEED ID(s) of the gene(s) it contains .<br> :Spreadsheet cells in the same row that contain rectangles of the same color represent genes that are clustered.<br> :A colored rectangle with an adjacent triangle indicate multiple genes are associated with this role.<br> :A white rectangle with a number indicates an unclustered gene(s) is associated with this role. The number indicates the number of genes.<br> :A black triangle indicates that there are more than five clusters of genes present in this genome for this subsystem.<br> Notes :The notes page contains explanations of the variant codes, references and additional information about this subsystem. 6d1b94fc42990ee60b9dea692b49a580577dde14 1569 1568 2006-11-07T18:56:47Z Mkubal 15 wikitext text/x-wiki SEED Viewer Subsystem Page Use the 'This Subsystem' menu in the green bar at the top of the page to view the 'Populated Subsystem' spreadsheet or to 'View Notes' for this susbystem.<br> or to return to the 'Overview'. Overview :On the top, right of the page a box contains the statistics for this subsystem including the<br> :number of functional roles, total number of genomes, and the number of genomes where this subsystem<br> :is present,not present or is still a work in progress. :The username of annotator who is responsible for the subsystem is listed. Diagram :The diagram illustrates the connectivity of the roles, alternate pathways, intermediate compounds and cofactors. :The functional role abbreviations in the boxes reference the roles in the table below. Currently diagrams are not present for every subsystem. Functional Roles Table :This list all the functional roles that define the subsystem. Each functional role is linked to a Functional Role page in the SEED Viewer.<br> :When present the entry in the EC column links to KEGG. :In the Ontologies column, the buttons 'Rc' and 'GO' are shaded green if a KEGG reaction<br> :or GO ontology term respectively is associated with this functional role. The 'Rc' button is linked to back to the Functional Role page<br> :which displays the KEGG reaction id. The 'GO' button is linked to an entry in AmiGO. :Functional roles that share the same abbreviation in the Group Alias column have been grouped together by the annotator, usually because<br> :they share a similar function but are found in different organisms. These groupings can be utilized in visualizing the Populated Subsystem table.<br> :If the annotator of the subsytem has defined subsets of functional roles, the 'Highlight subsets' menu will be present above the table. Use this menu<br> :to highlight the roles in the table that define internal pathways of the subsystem.<br> Populated Subsystem :By default this spreadsheet shows only genomes that possess a functional variant of this subsystem.<br> :An explanation of number in the Variant column is found by selecting 'View Notes' under the 'This Subsystem' menu in the green bar at the top of the page. :At the bottom of the page, checking the box 'Show organisms classified as not present in this subsystem' or 'Show organisms classified as work in progress' and clicking the 'Refresh populated subsystem' button, will update the spreadsheet with these genomes.<br> :Use the 'Limit genomes by taxonomy' menu, followed by the refresh button to limit the table to a specific group of organisms.<br> :Use the 'Collapse/Expand Group Aliases' button to combine or separate columns that are in the same group.(not yet implemented)<br> :Hovering over any element in a cell will display the SEED ID(s) of the gene(s) it contains .<br> :Spreadsheet cells in the same row that contain rectangles of the same color represent genes that are clustered.<br> :A colored rectangle with an adjacent triangle indicate multiple genes are associated with this role.<br> :A white rectangle with a number indicates an unclustered gene(s) is associated with this role. The number indicates the number of genes.<br> :A black triangle indicates that there are more than five clusters of genes present in this genome for this subsystem.<br> Notes :The notes page contains explanations of the variant codes, references and additional information about this subsystem. a0bd1cdb26c46b14eb3ebd03fd017ebcec580d66 1572 1569 2006-11-07T19:09:39Z Mkubal 15 wikitext text/x-wiki SEED Viewer Subsystem Page Use the 'This Subsystem' menu in the green bar at the top of the page to view the 'Populated Subsystem' spreadsheet or to 'View Notes' for this susbystem.<br> or to return to the 'Overview'. Overview :On the top, right of the page a box contains the statistics for this subsystem including the<br> :number of functional roles, total number of genomes, and the number of genomes where this subsystem<br> :is present,not present or is still a work in progress. :The username of annotator who is responsible for the subsystem is listed. Diagram :The diagram illustrates the connectivity of the roles, alternate pathways, intermediate compounds and cofactors. :The functional role abbreviations in the boxes reference the roles in the table below. Currently diagrams are not present for every subsystem. Functional Roles Table :This list all the functional roles that define the subsystem. Each functional role is linked to a Functional Role page in the SEED Viewer.<br> :When present the entry in the EC column links to KEGG. :In the Ontologies column, the buttons 'Rc' and 'GO' are shaded green if a KEGG reaction<br> :or GO ontology term respectively is associated with this functional role. The 'Rc' button is linked to back to the Functional Role page<br> :which displays the KEGG reaction id. The 'GO' button is linked to an entry in AmiGO. :Functional roles that share the same abbreviation in the Group Alias column have been grouped together by the annotator, usually because<br> :they share a similar function but are found in different organisms. These groupings can be utilized in visualizing the Populated Subsystem table.<br> :If the annotator of the subsytem has defined subsets of functional roles, the 'Highlight subsets' menu will be present above the table. Use this menu<br> :to highlight the roles in the table that define internal pathways of the subsystem.<br> Populated Subsystem :By default this spreadsheet shows only genomes that possess a functional variant of this subsystem.<br> :The taxonomy ID in the organism column is linked to an Organism page in the SEED Viewer.<br> :An explanation of number in the Variant column is found by selecting 'View Notes' under the 'This Subsystem' menu in the green bar at the top of the page. :At the bottom of the page, checking the box 'Show organisms classified as not present in this subsystem' or 'Show organisms classified as work in progress' and clicking the 'Refresh populated subsystem' button, will update the spreadsheet with these genomes.<br> :Use the 'Limit genomes by taxonomy' menu, followed by the refresh button to limit the table to a specific group of organisms.<br> :Use the 'Collapse/Expand Group Aliases' button to combine or separate columns that are in the same group.(not yet implemented)<br> :Hovering over any element in a cell will display the SEED ID(s) of the gene(s) it contains .<br> :Spreadsheet cells in the same row that contain rectangles of the same color represent genes that are clustered.<br> :A colored rectangle with an adjacent triangle indicate multiple genes are associated with this role.<br> :A white rectangle with a number indicates an unclustered gene(s) is associated with this role. The number indicates the number of genes.<br> :A black triangle indicates that there are more than five clusters of genes present in this genome for this subsystem.<br> Notes :The notes page contains explanations of the variant codes, references and additional information about this subsystem. 1ab8474b3674f212b566c9de47488a7e9888cf2d 0 1384 1570 1551 2006-11-07T19:05:30Z Mkubal 15 wikitext text/x-wiki ===General Features and Conventions of SeedViewer=== :Menus in the green bar at the top of every SEED Viewer page list options for interacting with the page. :Tool tips - [?] indicates a tool tip will appear when hovered above with the mouse. Underlined [?] indicates a clickable tool tip <br> :that also links into a wiki page for a more detailed explanation :Text Entry Boxes - if the text box has a pulldown menu beneath it, as text is entered in the box the menu will be updated with only items<br> :that match or contain the entered text. :Filtering Table Entries - filter the table by typing in text entry boxes in the column headers and hitting enter. Table entries that contain the typed text<br> :will remain. :Sorting Table Entries - alpahnumerically sort or reverse sort with the respective triangle in a column header :Browsing Table Entries - use the next>> and last>> links to quickly browse tables with more than 10 rows ===For a description of how to use the features on the different Seed Viewer pages, please follow the links below:=== :[[SeedViewer_Home| Home page]] :[[SeedViewer_Organism| Organism page]] :[[SeedViewer_Annotation| Annotation page]] :[[SeedViewer_Functional_Role| Functional Role page]] :[[SeedViewer_Subsystem| Subsystem page]] ===For tutorials on accomplishing specific tasks, please follow the link below:=== :[[SeedViewer_Tutorial| Tutorials]] 1ff1268ff3ed7b709185e6861420f8cfa815885f 0 1389 1571 1555 2006-11-07T19:07:08Z Mkubal 15 wikitext text/x-wiki SEED Viewer Functional Role Page In the top right corner of this page are statistics on the number of protein encoding genes within the SEED database that currently are<br> associated with this functional role and within how many different organisms these genes are present. ccb3e34f26750a6eddffe74b18b2b2701decd643 1573 1571 2006-11-07T19:22:09Z Mkubal 15 wikitext text/x-wiki SEED Viewer Functional Role Page In the top right corner of this page are statistics on the number of protein encoding genes within the SEED database that currently are<br> associated with this functional role and within how many different organisms these genes are present. This page list the subsystem(s) for a functional role and if present, EC number, associated GO terms, and KEGG reaction. A table list all occurences of the functional role in the SEED database. Refer to [[]SeedViewer_HowTo]] for table manipulation. ef7656bcc27fe1089efdc8e7e546550189a681f0 1574 1573 2006-11-07T19:23:56Z Mkubal 15 wikitext text/x-wiki SEED Viewer Functional Role Page In the top right corner of this page are statistics on the number of protein encoding genes within the SEED database that currently are<br> associated with this functional role and within how many different organisms these genes are present. This page list the subsystem(s) for a functional role and if present, EC number, associated GO terms, and KEGG reaction. A table list all occurences of the functional role in the SEED database. Click [[SeedViewer_HowTo|here ]] for table manipulation tips. 670e4cc8e1cb5810a2ccdf45e5ef82339c134bab 0 1385 1575 1539 2006-11-07T19:35:18Z Mkubal 15 wikitext text/x-wiki ===Counts of Genomes in the SEED=== The SEED contains archeal, bacterial, eukaryal, and viral genomes, as well as environmental samples.<br> A box on the top right of the home page provides a current total and complete count of each type. ===Searching=== The SEED Viewer's home page provides 4 different perspectives on searching to help you effciently access the data in the SEED.<br> By clicking on 'Text Search','BLAST Search', 'Subsystems' or 'Organisms' you can change the search perspective.<br> Notice that the text on button to the right of the text entry box will change after clicking on one of these perspectives. Text Search<br> :This is the default search option. Enter a key word or phrase in the text box and click the 'Text Search' button to the right of the text box.<br> :The search will treat the entered text as a regular expression and match strings and substrings found in functional roles, subsystems and features. :The results of the search will be displayed in up to 4 tables, a Functional Role table, Subsystem table,Features table and Organisms table.<br> :If a search returns only a single match, the appropriate SEED Viewer page will be displayed and the intermediate search results page with the tables<br> :mentioned above will not be displayed. :The number of hits associated with a functional role will appear above the Functional Role table. <br> :The number of features returned is limited to 100. <br> :To browse the results quickly use the next >> and last >> links. :The columns in all tables can be alphanumerically sorted and reverse sorted by clicking on the respective triangle in a column header.<br> :If you check the 'quick search' option, the results will be limited to functionals role in a subsystem. :In any of the results tables, :clicking on a functional role will take you to a Functional Role page in the SEED Viewer, :clicking on a subsystem will take you to a Subsystem page in the SEED Viewer and :clicking on a PEG ID will take you an Annotation page in the SEED Viewer. Blast Search<br> : Enter a DNA or amino acid sequence, and select a genome from the pulldown menu above the text box. You must select a genome.<br> : Then click the 'Blast Search' button to the right of the genome pulldown menu. : The results will be in typical Blast output format and include PEG IDs that are linked to an Annotation page in the SEED Viewer. Subsystems Search<br> :Selecting this option provides an alphanumerically sorted pulldown menu of subsystems in the SEED and also a text entry box.<br> :Notice as you type in text entry box the pulldown menu is automatically updated with subsystems that contain the entered text,<br> :and not just matching at the beginning of the subsystem name. :After selecting a subsystem, clicking the 'View Subsystem' button will take you a Subsystem page in the SEED Viewer. Organism Search<br> :Selecting this option provides an alphabetized pulldown menu of genomes in the SEED and also a text entry box.<br> :Notice as you type in text entry box the pulldown menu is automatically updated with genomes that contain the entered text,<br> :and not just matching at the beginning of the genome. :After selecting an organism, clicking the 'View Organism' button will take you an organism page in the SEED Viewer. 6a273e17f1caf7bdf72afaa978ed8a70c100d010 1576 1575 2006-11-07T19:37:16Z Mkubal 15 wikitext text/x-wiki ===Counts of Genomes in the SEED=== The SEED contains archeal, bacterial, eukaryal, and viral genomes, as well as environmental samples.<br> A box on the top right of the home page provides a current total and complete count of each type. ===Searching=== The SEED Viewer's home page provides 4 different perspectives on searching to help you effciently access the data in the SEED.<br> By clicking on 'Text Search','BLAST Search', 'Subsystems' or 'Organisms' you can change the search perspective.<br> Notice that the text on button to the right of the text entry box will change after clicking on one of these perspectives. Text Search<br> :This is the default search option. Enter a key word or phrase in the text box and click the 'Text Search' button to the right of the text box.<br> :The search will treat the entered text as a regular expression and match strings and substrings found in functional roles, subsystems and features. :The results of the search will be displayed in up to 4 tables, a Functional Role table, Subsystem table,Features table and Organisms table.<br> :If a search returns only a single match, the appropriate SEED Viewer page will be displayed and the intermediate search results page with the tables<br> :mentioned above will not be displayed. :The number of hits associated with a functional role will appear above the Functional Role table. <br> :The number of features returned is limited to 100. <br> :To browse the results quickly use the next >> and last >> links. :The columns in all tables can be alphanumerically sorted and reverse sorted by clicking on the respective triangle in a column header.<br> :If you check the 'quick search' option, the results will be limited to functionals role in a subsystem. :In any of the results tables, :clicking on a functional role will take you to a Functional Role page in the SEED Viewer, :clicking on a subsystem will take you to a Subsystem page in the SEED Viewer and :clicking on a feature ID will take you an Annotation page in the SEED Viewer. Blast Search<br> : Enter a DNA or amino acid sequence, and select a genome from the pulldown menu above the text box. You must select a genome.<br> : Then click the 'Blast Search' button to the right of the genome pulldown menu. : The results will be in typical Blast output format and include PEG IDs that are linked to an Annotation page in the SEED Viewer. Subsystems Search<br> :Selecting this option provides an alphanumerically sorted pulldown menu of subsystems in the SEED and also a text entry box.<br> :Notice as you type in text entry box the pulldown menu is automatically updated with subsystems that contain the entered text,<br> :and not just matching at the beginning of the subsystem name. :After selecting a subsystem, clicking the 'View Subsystem' button will take you a Subsystem page in the SEED Viewer. Organism Search<br> :Selecting this option provides an alphabetized pulldown menu of genomes in the SEED and also a text entry box.<br> :Notice as you type in text entry box the pulldown menu is automatically updated with genomes that contain the entered text,<br> :and not just matching at the beginning of the genome. :After selecting an organism, clicking the 'View Organism' button will take you an organism page in the SEED Viewer. 1f732f2135c756946baf0386876a59977108cf6a 1581 1576 2006-11-07T20:08:11Z Mkubal 15 wikitext text/x-wiki ===Counts of Genomes in the SEED=== The SEED contains archeal, bacterial, eukaryal, and viral genomes, as well as environmental samples.<br> A box on the top right of the home page provides a current total and complete count of each type. <>br> Click on archael, bacterial. eukaryal, or viral to display a table listing the genomes in this set.<br> ===Searching=== The SEED Viewer's home page provides 4 different perspectives on searching to help you effciently access the data in the SEED.<br> By clicking on 'Text Search','BLAST Search', 'Subsystems' or 'Organisms' you can change the search perspective.<br> Notice that the text on button to the right of the text entry box will change after clicking on one of these perspectives. Text Search<br> :This is the default search option. Enter a key word or phrase in the text box and click the 'Text Search' button to the right of the text box.<br> :The search will treat the entered text as a regular expression and match strings and substrings found in functional roles, subsystems and features. :The results of the search will be displayed in up to 4 tables, a Functional Role table, Subsystem table,Features table and Organisms table.<br> :If a search returns only a single match, the appropriate SEED Viewer page will be displayed and the intermediate search results page with the tables<br> :mentioned above will not be displayed. :The number of hits associated with a functional role will appear above the Functional Role table. <br> :The number of features returned is limited to 100. <br> :To browse the results quickly use the next >> and last >> links. :The columns in all tables can be alphanumerically sorted and reverse sorted by clicking on the respective triangle in a column header.<br> :If you check the 'quick search' option, the results will be limited to functionals role in a subsystem. :In any of the results tables, :clicking on a functional role will take you to a Functional Role page in the SEED Viewer, :clicking on a subsystem will take you to a Subsystem page in the SEED Viewer and :clicking on a feature ID will take you an Annotation page in the SEED Viewer. Blast Search<br> : Enter a DNA or amino acid sequence, and select a genome from the pulldown menu above the text box. You must select a genome.<br> : Then click the 'Blast Search' button to the right of the genome pulldown menu. : The results will be in typical Blast output format and include PEG IDs that are linked to an Annotation page in the SEED Viewer. Subsystems Search<br> :Selecting this option provides an alphanumerically sorted pulldown menu of subsystems in the SEED and also a text entry box.<br> :Notice as you type in text entry box the pulldown menu is automatically updated with subsystems that contain the entered text,<br> :and not just matching at the beginning of the subsystem name. :After selecting a subsystem, clicking the 'View Subsystem' button will take you a Subsystem page in the SEED Viewer. Organism Search<br> :Selecting this option provides an alphabetized pulldown menu of genomes in the SEED and also a text entry box.<br> :Notice as you type in text entry box the pulldown menu is automatically updated with genomes that contain the entered text,<br> :and not just matching at the beginning of the genome. :After selecting an organism, clicking the 'View Organism' button will take you an organism page in the SEED Viewer. 5556e32f5309368bde8aa47d5f8109cba17eabaf 1582 1581 2006-11-07T20:08:31Z Mkubal 15 wikitext text/x-wiki ===Counts of Genomes in the SEED=== The SEED contains archeal, bacterial, eukaryal, and viral genomes, as well as environmental samples.<br> A box on the top right of the home page provides a current total and complete count of each type.<br> Click on archael, bacterial. eukaryal, or viral to display a table listing the genomes in this set.<br> ===Searching=== The SEED Viewer's home page provides 4 different perspectives on searching to help you effciently access the data in the SEED.<br> By clicking on 'Text Search','BLAST Search', 'Subsystems' or 'Organisms' you can change the search perspective.<br> Notice that the text on button to the right of the text entry box will change after clicking on one of these perspectives. Text Search<br> :This is the default search option. Enter a key word or phrase in the text box and click the 'Text Search' button to the right of the text box.<br> :The search will treat the entered text as a regular expression and match strings and substrings found in functional roles, subsystems and features. :The results of the search will be displayed in up to 4 tables, a Functional Role table, Subsystem table,Features table and Organisms table.<br> :If a search returns only a single match, the appropriate SEED Viewer page will be displayed and the intermediate search results page with the tables<br> :mentioned above will not be displayed. :The number of hits associated with a functional role will appear above the Functional Role table. <br> :The number of features returned is limited to 100. <br> :To browse the results quickly use the next >> and last >> links. :The columns in all tables can be alphanumerically sorted and reverse sorted by clicking on the respective triangle in a column header.<br> :If you check the 'quick search' option, the results will be limited to functionals role in a subsystem. :In any of the results tables, :clicking on a functional role will take you to a Functional Role page in the SEED Viewer, :clicking on a subsystem will take you to a Subsystem page in the SEED Viewer and :clicking on a feature ID will take you an Annotation page in the SEED Viewer. Blast Search<br> : Enter a DNA or amino acid sequence, and select a genome from the pulldown menu above the text box. You must select a genome.<br> : Then click the 'Blast Search' button to the right of the genome pulldown menu. : The results will be in typical Blast output format and include PEG IDs that are linked to an Annotation page in the SEED Viewer. Subsystems Search<br> :Selecting this option provides an alphanumerically sorted pulldown menu of subsystems in the SEED and also a text entry box.<br> :Notice as you type in text entry box the pulldown menu is automatically updated with subsystems that contain the entered text,<br> :and not just matching at the beginning of the subsystem name. :After selecting a subsystem, clicking the 'View Subsystem' button will take you a Subsystem page in the SEED Viewer. Organism Search<br> :Selecting this option provides an alphabetized pulldown menu of genomes in the SEED and also a text entry box.<br> :Notice as you type in text entry box the pulldown menu is automatically updated with genomes that contain the entered text,<br> :and not just matching at the beginning of the genome. :After selecting an organism, clicking the 'View Organism' button will take you an organism page in the SEED Viewer. 4aefa283823c70ac0cd53dc45edc6fd8b6e07a3d 1583 1582 2006-11-07T20:09:34Z Mkubal 15 wikitext text/x-wiki ===Counts of Genomes in the SEED=== The SEED contains archeal, bacterial, eukaryal, and viral genomes, as well as environmental samples.<br> A box on the top right of the home page provides a current total and complete count of each type.<br> Click on archael, bacterial, eukaryal, or viral to display a table listing the genomes in this set.<br> ===Searching=== The SEED Viewer's home page provides 4 different perspectives on searching to help you effciently access the data in the SEED.<br> By clicking on 'Text Search','BLAST Search', 'Subsystems' or 'Organisms' you can change the search perspective.<br> Notice that the text on button to the right of the text entry box will change after clicking on one of these perspectives. Text Search<br> :This is the default search option. Enter a key word or phrase in the text box and click the 'Text Search' button to the right of the text box.<br> :The search will treat the entered text as a regular expression and match strings and substrings found in functional roles, subsystems and features. :The results of the search will be displayed in up to 4 tables, a Functional Role table, Subsystem table,Features table and Organisms table.<br> :If a search returns only a single match, the appropriate SEED Viewer page will be displayed and the intermediate search results page with the tables<br> :mentioned above will not be displayed. :The number of hits associated with a functional role will appear above the Functional Role table. <br> :The number of features returned is limited to 100. <br> :To browse the results quickly use the next >> and last >> links. :The columns in all tables can be alphanumerically sorted and reverse sorted by clicking on the respective triangle in a column header.<br> :If you check the 'quick search' option, the results will be limited to functionals role in a subsystem. :In any of the results tables, :clicking on a functional role will take you to a Functional Role page in the SEED Viewer, :clicking on a subsystem will take you to a Subsystem page in the SEED Viewer and :clicking on a feature ID will take you an Annotation page in the SEED Viewer. Blast Search<br> : Enter a DNA or amino acid sequence, and select a genome from the pulldown menu above the text box. You must select a genome.<br> : Then click the 'Blast Search' button to the right of the genome pulldown menu. : The results will be in typical Blast output format and include PEG IDs that are linked to an Annotation page in the SEED Viewer. Subsystems Search<br> :Selecting this option provides an alphanumerically sorted pulldown menu of subsystems in the SEED and also a text entry box.<br> :Notice as you type in text entry box the pulldown menu is automatically updated with subsystems that contain the entered text,<br> :and not just matching at the beginning of the subsystem name. :After selecting a subsystem, clicking the 'View Subsystem' button will take you a Subsystem page in the SEED Viewer. Organism Search<br> :Selecting this option provides an alphabetized pulldown menu of genomes in the SEED and also a text entry box.<br> :Notice as you type in text entry box the pulldown menu is automatically updated with genomes that contain the entered text,<br> :and not just matching at the beginning of the genome. :After selecting an organism, clicking the 'View Organism' button will take you an organism page in the SEED Viewer. 33fc0190ed9856a11f1cfb4aa69498addac51b40 0 1388 1577 1554 2006-11-07T19:45:39Z Mkubal 15 wikitext text/x-wiki SEED Viewer Annotation Page Overview :This page offers access to the data relating to a feature. By default the Overview version of the page <br> :is initially displayed providing the feature's function assignment, source organism, the role it performs<br> :in a subsystem, and a graphic displaying it's genomic context. :Detailed information about this feature's role or roles in one or more subsystems is provided in a shaded<br> :at the top of the page on the right. The functional role names and subsystem names are linked to the <br> :[[SeedViewer_Functional_Role|SEED Viewer Functional Role page]] and the [[SeedViewer_Subsystem|SEED Viewer Subsystem page]]. :In the graphic each line represents a different genome. The genome of the feature that is the subject of this page<br> :is on the first line with the subject feature in red and centered in a 16kb window. Features on the same line that have<br> :a gray shadow are functionally coupled to the subject feature. Features in different genome that share the same color or <br> :number are similar. Clicking 'Diverse Genomes' will change the genomes in the graphic to a set that is more phylogentically<br> :distant to the subject feature's genome. Sequence Data :From the green bar at the top of page, selecting the 'This Protein' menu will give the user the choice of viewing the<br> :this feature's DNA sequence, DNA with flanking sequence or amino acid sequence. Tools :From the green bar at the top of the page, selecting the 'Tools' menu will give the user the choice of the following tools<br> :to analyze this feature:<br> ::TMpred ::TMHMM ::Gram negative PSORT ::Gram negative SignalP ::Gram positive PSORT ::Gram positive SignalP ::LipoP ::InterProScan ::Radar ::PPSearch ::Gram negative CELLO ::Gram positive CELLO ::ProDom Literature d94ec135e813aef2d0ad72d09d14ef2caa34943b 1578 1577 2006-11-07T19:54:13Z Mkubal 15 wikitext text/x-wiki SEED Viewer Annotation Page Overview :This page offers access to the data relating to a feature. By default the Overview version of the page <br> :is initially displayed providing the feature's function assignment, source organism, the role it performs<br> :in a subsystem, and a graphic displaying it's genomic context. If this feature's function is associated with one<br> :or more functional roles, each functional role's name will be displayed and linked to a [[SeedViewer_Functional_Role|SEED Viewer Functional Role page]]. :If this feature is included in a subsystem detailed information about this feature's role or roles in one or more subsystems is provided in a shaded box <br> :at the top of the page on the right. The functional role names and subsystem names are linked to the <br> :[[SeedViewer_Functional_Role|SEED Viewer Functional Role page]] and the [[SeedViewer_Subsystem|SEED Viewer Subsystem page]]. :In the graphic each line represents a different genome. The genome of the feature that is the subject of this page<br> :is on the first line with the subject feature in red and centered in a 16kb window. Features on the same line that have<br> :a gray shadow are functionally coupled to the subject feature. Features in different genome that share the same color or <br> :number are similar. Clicking 'Diverse Genomes' will change the genomes in the graphic to a set that is more phylogentically<br> :distant to the subject feature's genome. Sequence Data :From the green bar at the top of page, selecting the 'This Protein' menu will give the user the choice of viewing the<br> :this feature's DNA sequence, DNA with flanking sequence or amino acid sequence. Tools :From the green bar at the top of the page, selecting the 'Tools' menu will give the user the choice of the following tools<br> :to analyze this feature:<br> ::TMpred ::TMHMM ::Gram negative PSORT ::Gram negative SignalP ::Gram positive PSORT ::Gram positive SignalP ::LipoP ::InterProScan ::Radar ::PPSearch ::Gram negative CELLO ::Gram positive CELLO ::ProDom Literature 531fb3a3d6ce04818344461624881d292837b9bc 1579 1578 2006-11-07T20:00:46Z Mkubal 15 wikitext text/x-wiki SEED Viewer Annotation Page Overview :This page offers access to the data relating to a feature. By default the Overview version of the page <br> :is initially displayed providing the feature's function assignment, source organism, the role it performs<br> :in a subsystem, and a graphic displaying it's genomic context. If this feature's function is associated with one<br> :or more functional roles, each functional role's name will be displayed and linked to a [[SeedViewer_Functional_Role|SEED Viewer Functional Role page]]. :A part of a feature's function that is not also a functional role is NOT linked. :If this feature is included in a subsystem detailed information about this feature's role or roles in one or more subsystems is provided in a shaded box <br> :at the top of the page on the right. The functional role names and subsystem names are linked to the <br> :[[SeedViewer_Functional_Role|SEED Viewer Functional Role page]] and the [[SeedViewer_Subsystem|SEED Viewer Subsystem page]]. :In the graphic each line represents a different genome. The genome of the feature that is the subject of this page<br> :is on the first line with the subject feature in red and centered in a 16kb window. Features on the same line that have<br> :a gray shadow are functionally coupled to the subject feature. Features in different genome that share the same color or <br> :number are similar. Clicking 'Diverse Genomes' will change the genomes in the graphic to a set that is more phylogentically<br> :distant to the subject feature's genome. Sequence Data :From the green bar at the top of page, selecting the 'This Protein' menu will give the user the choice of viewing the<br> :this feature's DNA sequence, DNA with flanking sequence or amino acid sequence. Tools :From the green bar at the top of the page, selecting the 'Tools' menu will give the user the choice of the following tools<br> :to analyze this feature:<br> ::TMpred ::TMHMM ::Gram negative PSORT ::Gram negative SignalP ::Gram positive PSORT ::Gram positive SignalP ::LipoP ::InterProScan ::Radar ::PPSearch ::Gram negative CELLO ::Gram positive CELLO ::ProDom Literature bc7facb3fa0443ae3c9b1be78571e631527d9edf 1580 1579 2006-11-07T20:03:35Z Mkubal 15 wikitext text/x-wiki SEED Viewer Annotation Page Overview :This page offers access to the data relating to a feature. By default the Overview version of the page <br> :is initially displayed providing the feature's function assignment, source organism, the role it performs<br> :in a subsystem, and a graphic displaying it's genomic context. If this feature's function is associated with one<br> :or more functional roles, each functional role's name will be displayed and linked to a [[SeedViewer_Functional_Role|SEED Viewer Functional Role page]]. :A part of a feature's function that is not also a functional role is NOT linked. :If this feature is included in a subsystem detailed information about this feature's role or roles in one or more subsystems is provided in a shaded box <br> :at the top of the page on the right. The functional role names and subsystem names are linked to the <br> :[[SeedViewer_Functional_Role|SEED Viewer Functional Role page]] and the [[SeedViewer_Subsystem|SEED Viewer Subsystem page]]. :In the graphic each line represents a different genome. The genome of the feature that is the subject of this page<br> :is on the first line with the subject feature in red and centered in a 16kb window. Features on the same line that have<br> :a gray shadow are functionally coupled to the subject feature. Features in different genome that share the same color or <br> :number are similar. Clicking 'Diverse Genomes' will change the genomes in the graphic to a set that is more phylogentically<br> :distant to the subject feature's genome. Sequence Data :From the green bar at the top of page, selecting the 'This Protein' menu will give the user the choice of viewing the<br> :this feature's DNA sequence, DNA with flanking sequence or amino acid sequence. Tools :From the green bar at the top of the page, selecting the 'Tools' menu will give the user the choice of the following tools<br> :to analyze this feature:<br> ::TMpred ::TMHMM ::Gram negative PSORT ::Gram negative SignalP ::Gram positive PSORT ::Gram positive SignalP ::LipoP ::InterProScan ::Radar ::PPSearch ::Gram negative CELLO ::Gram positive CELLO ::ProDom Literature :This menu list links to sources of literature discussing this specific feature. Currently PubMed is the only source. 93e1d8b93f91e31ed9308931bbb55c0ece03e66b 1585 1580 2006-11-07T20:24:51Z Mkubal 15 wikitext text/x-wiki SEED Viewer Annotation Page Overview :This page offers access to the data relating to a feature. By default the Overview version of the page <br> :is initially displayed providing the feature's function assignment, source organism, the role it performs<br> :in a subsystem, and a graphic displaying it's genomic context. If this feature's function is associated with one<br> :or more functional roles, each functional role's name will be displayed and linked to a [[SeedViewer_Functional_Role|SEED Viewer Functional Role page]]. :A part of a feature's function that is not also a functional role is NOT linked. :If this feature is included in a subsystem detailed information about this feature's role or roles in one or more subsystems is provided in a shaded box <br> :at the top of the page on the right. The functional role names and subsystem names are linked to the <br> :[[SeedViewer_Functional_Role|SEED Viewer Functional Role page]] and the [[SeedViewer_Subsystem|SEED Viewer Subsystem page]]. :In the graphic each line represents a different genome. The genome of the feature that is the subject of this page<br> :is on the first line with the subject feature in red and centered in a 16kb window. Features on the same line that have<br> :a gray shadow are functionally coupled to the subject feature. Features in different genome that share the same color or <br> :number are similar. Clicking 'Diverse Genomes' will change the genomes in the graphic to a set that is more phylogentically<br> :distant to the subject feature's genome. :If there are no close genomes only a single line for the subject feature's genome will be present.<br> :If no data for diverse genomes has been computed a message saying so will be be displayed.<br> Sequence Data :From the green bar at the top of page, selecting the 'This Protein' menu will give the user the choice of viewing the<br> :this feature's DNA sequence, DNA with flanking sequence or amino acid sequence. Tools :From the green bar at the top of the page, selecting the 'Tools' menu will give the user the choice of the following tools<br> :to analyze this feature:<br> ::TMpred ::TMHMM ::Gram negative PSORT ::Gram negative SignalP ::Gram positive PSORT ::Gram positive SignalP ::LipoP ::InterProScan ::Radar ::PPSearch ::Gram negative CELLO ::Gram positive CELLO ::ProDom Literature :This menu list links to sources of literature discussing this specific feature. Currently PubMed is the only source. 14624d8aac8c4c02472c1c340c98e081bc06a0e1 0 1386 1584 1549 2006-11-07T20:16:21Z Mkubal 15 wikitext text/x-wiki Organism Page in SEED Viewer In the green bar at the top of the page adjacent to the homepage symbol is a pulldown menu<br> labeled 'This Organism' with the following 4 display options for this page:<br> Overview :The top of page provides summary statistics for this genome including the numbers of subsystems, coding sequences, RNAs and other background information.<br> :A breakdown of the number of protein encoding genes with hypothetical and non-hypothetical function assignments is provided in box in the top right corner of the page.<br> :Adjacent to the Taxonomy ID is the Wikipedia Globe that is linked to the Wikipedia entry for this organism. :On the bottom left of the page a bar graph depicts the percentages of protein encoding genes for this genome that are present in at least one subsystem.<br> :Next to the bar graph a pie chart and accompanying expandable hierarchical tree, color coded to match the pie chart, organizes the subsystems<br> :present in this genome by cellular process. :At every level in the tree the number of protein encoding genes in each category is listed in parentheses. :At the leaves of the tree are links to a Subsytem page in the SEED Viewer. Browse Genome :This display allows you to walk the chromosome of the selected genome.<br> :If the genome is not completely assembled, the first contig will be selected. :The window size in terms of number of base pairs can be selected using the 'Window Size' pulldown menu, or the 'zoom in' or 'zoom out' buttons.<br> :The < and > buttons will move the window down or up the chromosome half the window size.<br> :The << and >> buttons will move the window down or up the chromosome a full window size.<br> :Under 'Options' you can select which features and the number of strands or reading frames displayed. By default the genome browser offers a two strand view of the currently selected organism.<br> :After selecting your options, click the 'Refresh' button to update the page. :On the middle line of the chromosome display you will see features not associated with a reading frame, such as rnas, pathogenicity islands or prophages.<br> :Hover over a feature in the chromosome display for a detailed description. :Clicking an item will take you to the Annotation page in the SEED Viewer for this feature. View Features :Selecting this display provides a table containing feature ID, functional assignment, starting and stopping location in terms of base pairs relative<br> :to the beginning of the contig, feature type and a list of aliases.<br> :The total number of features for this genome is displayed above the table.<br> :Use the 'next>>' and 'last>>' links to quickly scroll through sets of 10 features.<br> :Filter features across the entire genome by using the text entry boxes in the 'Functional Assignment', 'Type' or 'Aliases' column header and then hitting enter. :Sort or reverse sort the tables using the triangle in the columns headers. :Export all or a subset of the features, after filtering, of a genome to a spreadsheet file using the 'Export Table' button. View Reactions 32e3e34618a9d984764d199d29b16253352f0679 0 1371 1586 1470 2006-11-14T13:52:12Z RobEdwards 14 wikitext text/x-wiki == SEED standard operating procedures == To generate data that is useful to the various communities involved in the process of annotation and use of annotations, we make available out standard operating procedures. * [[GeneCalling|Gene calling]] * Annotation ** [[Annotation_of_close_strain_sets|Annotation of close strain sets]] ** Annotation of diverse genomes. *BRC **[[Release_to_BRC|Releasing GFF3 files]] -- Creating and uploaing GFF3 files 54605e25dc132c89d0711d6d23c32c438c2dc47f 1590 1586 2006-11-15T21:11:34Z TerryDisz 4 /* SEED standard operating procedures */ wikitext text/x-wiki == SEED standard operating procedures == To generate data that is useful to the various communities involved in the process of annotation and use of annotations, we make available out standard operating procedures. * [[GeneCalling|Gene calling]] * Annotation ** [[Annotation_of_close_strain_sets|Annotation of close strain sets]] ** Annotation of diverse genomes. *BRC **[[Release_to_BRC|Releasing GFF3 files]] -- Creating and uploading GFF3 files 8e26e1ab0de7687c2e18845dbeadb2c9a66f1a7e 1596 1590 2006-12-04T20:04:56Z FolkerMeyer 2 wikitext text/x-wiki == SEED standard operating procedures == To generate data that is useful to the various communities involved in the process of annotation and use of annotations, we make available our standard operating procedures. * Annotation ** Annotating a genome with the 48-hour service (FIG|SOP005) ** Creation of GO-terms (FIG|SOP004) *BRC **[[Release_to_BRC|Releasing GFF3 files(FIG|SOP003)]] -- Creating and uploading GFF3 files * Obsolete SOPs ** [[GeneCalling|Gene calling (FIG|SOP001)]] ** [[Annotation_of_close_strain_sets|Annotation of close strain sets(FIG|SOP002)]] 711d59f6a27ea0d1727a0607a0605d7c0bf359ea 1597 1596 2006-12-04T20:13:56Z TerryDisz 4 wikitext text/x-wiki == SEED standard operating procedures == To generate data that is useful to the various communities involved in the process of annotation and use of annotations, we make available our standard operating procedures. * Annotation ** Annotating a genome with the 48-hour service (NMPDR|SOP005) ** Creation of GO-terms (NMPDR|SOP004) *BRC **[[Release_to_BRC|Releasing GFF3 files(NMPDR|SOP003)]] -- Creating and uploading GFF3 files * Obsolete SOPs ** [[GeneCalling|Gene calling (NMPDR|SOP001)]] ** [[Annotation_of_close_strain_sets|Annotation of close strain sets(NMPDR|SOP002)]] 80fcc91c99d2b978564b2dc54eb7e3b09cc3e851 1598 1597 2006-12-04T20:21:31Z TerryDisz 4 wikitext text/x-wiki == SEED standard operating procedures == To generate data that is useful to the various communities involved in the process of annotation and use of annotations, we make available our standard operating procedures. * Annotation ** Annotating a genome with the 48-hour service (NMPDR|SOP005) ** Creation of GO-terms (NMPDR|SOP004) *BRC **[[Release_to_BRC|Releasing GFF3 files(NMPDR|SOP006)]] -- Creating and uploading GFF3 files * Obsolete SOPs ** [[GeneCalling|Gene calling (NMPDR|SOP001)]] ** [[Annotation_of_close_strain_sets|Annotation of close strain sets(NMPDR|SOP002)]] ** [[Adding Genomes to the NMPDR (NMPDR|SOP003)]] d14b91fbc820fec155ab554ef242e513bf746fd3 1602 1598 2006-12-04T20:54:14Z TerryDisz 4 wikitext text/x-wiki == SEED standard operating procedures == To generate data that is useful to the various communities involved in the process of annotation and use of annotations, we make available our standard operating procedures. * Annotation ** Annotating a genome with the 48-hour service (NMPDR|SOP005) ** Creation of GO-terms (NMPDR|SOP004) *BRC **[[Image:Brc upload sop.pdf|Releasing GFF3 files(NMPDR|SOP006)]] -- Creating and uploading GFF3 files * Obsolete SOPs ** [[GeneCalling|Gene calling (NMPDR|SOP001)]] ** [[Annotation_of_close_strain_sets|Annotation of close strain sets(NMPDR|SOP002)]] ** [[Adding Genomes|Adding Genomes to the NMPDR (NMPDR|SOP003)]] 0a16695666a47f00f0cc7982165dc9acdf99f13f 1610 1602 2006-12-04T21:56:04Z TerryDisz 4 wikitext text/x-wiki == SEED standard operating procedures == To generate data that is useful to the various communities involved in the process of annotation and use of annotations, we make available our standard operating procedures. * Annotation ** Annotating a genome with the 48-hour service (NMPDR|SOP005) ** Creation of GO-terms (NMPDR|SOP004) *BRC **[[Image:Brc upload sop.pdf|Releasing GFF3 files(NMPDR|SOP006)]] -- Creating and uploading GFF3 files * Obsolete SOPs ** [[GeneCalling|Gene calling (NMPDR|SOP001)]] ** [[Annotation_of_close_strain_sets|Annotation of close strain sets(NMPDR|SOP002)]] ** [[Image:New_genome_sop.pdf|Adding Genomes to the NMPDR (NMPDR|SOP003)]] 842c0b9ab5d565f27643c7b2027897db3e707743 1612 1610 2006-12-06T14:29:34Z TerryDisz 4 wikitext text/x-wiki == SEED standard operating procedures == To generate data that is useful to the various communities involved in the process of annotation and use of annotations, we make available our standard operating procedures. * Annotation ** [[Image:48hrserver.pdf|Annotating a genome with the 48-hour service (NMPDR|SOP005)]] ** Creation of GO-terms (NMPDR|SOP004) *BRC **[[Image:brc upload sop.pdf|Releasing GFF3 files(NMPDR|SOP006)]] * Obsolete SOPs ** [[GeneCalling|Gene calling (NMPDR|SOP001)]] ** [[Annotation_of_close_strain_sets|Annotation of close strain sets(NMPDR|SOP002)]] ** [[Image:New_genome_sop.pdf|Adding Genomes to the NMPDR (NMPDR|SOP003)]] b2bb93caf678b375521593d6d3bcab0631f2d73c 1614 1612 2006-12-06T14:31:33Z TerryDisz 4 wikitext text/x-wiki == SEED standard operating procedures == To generate data that is useful to the various communities involved in the process of annotation and use of annotations, we make available our standard operating procedures. * Annotation ** [[Image:The48hrserver.pdf|Annotating a genome with the 48-hour service (NMPDR|SOP005)]] ** Creation of GO-terms (NMPDR|SOP004) *BRC **[[Image:brc upload sop.pdf|Releasing GFF3 files(NMPDR|SOP006)]] * Obsolete SOPs ** [[GeneCalling|Gene calling (NMPDR|SOP001)]] ** [[Annotation_of_close_strain_sets|Annotation of close strain sets(NMPDR|SOP002)]] ** [[Image:New_genome_sop.pdf|Adding Genomes to the NMPDR (NMPDR|SOP003)]] 8a2ba6587c1d31ece71b2a2b9538dc983ee0bdf1 1615 1614 2006-12-06T14:34:10Z TerryDisz 4 wikitext text/x-wiki == SEED standard operating procedures == To generate data that is useful to the various communities involved in the process of annotation and use of annotations, we make available our standard operating procedures. * Annotation ** [[Image:The48hrserver.pdf|Annotating a genome with the 48-hour service (NMPDR|SOP005)]] Using the 48 hour server. ** Creation of GO-terms (NMPDR|SOP004) *BRC **[[Image:brc upload sop.pdf|Releasing GFF3 files(NMPDR|SOP006)]] * Obsolete SOPs ** [[GeneCalling|Gene calling (NMPDR|SOP001)]] ** [[Annotation_of_close_strain_sets|Annotation of close strain sets(NMPDR|SOP002)]] ** [[Image:New_genome_sop.pdf|Adding Genomes to the NMPDR (NMPDR|SOP003)]] d8203825249a3b12c97df95f6b4f9873f63ec615 1616 1615 2006-12-06T14:38:15Z TerryDisz 4 wikitext text/x-wiki == SEED standard operating procedures == To generate data that is useful to the various communities involved in the process of annotation and use of annotations, we make available our standard operating procedures. * Annotation ** [[Image:The48hrserver.pdf]]Annotating a genome with the 48-hour service (NMPDR|SOP005) ** Creation of GO-terms (NMPDR|SOP004) *BRC **[[Image:brc upload sop.pdf]]Releasing GFF3 files(NMPDR|SOP006) * Obsolete SOPs ** [[GeneCalling|Gene calling (NMPDR|SOP001)]] ** [[Annotation_of_close_strain_sets|Annotation of close strain sets(NMPDR|SOP002)]] ** [[Image:New_genome_sop.pdf]]Adding Genomes to the NMPDR (NMPDR|SOP003) 8443681d8d33044274740e4db8fae7f6d439dca3 1617 1616 2006-12-06T14:38:42Z TerryDisz 4 wikitext text/x-wiki == SEED standard operating procedures == To generate data that is useful to the various communities involved in the process of annotation and use of annotations, we make available our standard operating procedures. * Annotation ** [[Image:The48hrserver.pdf]] Annotating a genome with the 48-hour service (NMPDR|SOP005) ** Creation of GO-terms (NMPDR|SOP004) *BRC **[[Image:brc upload sop.pdf]] Releasing GFF3 files(NMPDR|SOP006) * Obsolete SOPs ** [[GeneCalling|Gene calling (NMPDR|SOP001)]] ** [[Annotation_of_close_strain_sets|Annotation of close strain sets(NMPDR|SOP002)]] ** [[Image:New_genome_sop.pdf]] Adding Genomes to the NMPDR (NMPDR|SOP003) a8aa5b06ba3d8a71bbc90180e3bdc39ca0440e29 0 1391 1587 2006-11-14T14:03:45Z RobEdwards 14 How to create and upload GFF3 files to the BRC wikitext text/x-wiki === How to Create and Release GFF3 files to the BRCs === We regularly release our data to BRC-central via GFF3 files. This page describes the steps to release the data. * Creating the files Choose a machine that is upto date, and create an empty directory. Run the command nmpdr2gff NMPDR This looks through all genomes for the NMPDR flag, and if it is found then a GFF3 file is created. If you suspect that files are not created for some genomes that should have them, then the NMPDR flag has not been set. Once complete you will have a directory structure that looks something like this (only the first two genomes are shown for each organism): *NMPDR **Campylobacter ***Campylobacter.coli.RM2228.gff3 ***Campylobacter.jejuni.subsp.jejuni.84-25.gff3 ***... **Listeria ***Listeria.innocua.Clip11262.gff3 ***Listeria.monocytogenes.EGD-e.gff3 ***... **Staphylococcus ***Staphylococcus.aureus.RF122.gff3 ***Staphylococcus.aureus.subsp.aureus.MRSA252.gff3 ***... **Streptococcus ***Streptococcus.pneumoniae.R6.gff3 ***Streptococcus.pyogenes.MGAS10270.gff3 ***... **Vibrio ***Vibrio.cholerae.MO10.gff3 ***Vibrio.cholerae.O395.gff3 ***... 71e5f714d231a19f4fbd354e4402dee566206282 1588 1587 2006-11-14T14:18:36Z RobEdwards 14 /* How to Create and Release GFF3 files to the BRCs */ wikitext text/x-wiki == How to Create and Release GFF3 files to the BRCs == We regularly release our data to BRC-central via GFF3 files. This page describes the steps to release the data. ===Creating the files=== Choose a machine that is upto date, and create an empty directory. For this example, we'll use the directory NMPDR Run the command nmpdr2gff NMPDR This looks through all genomes for the NMPDR flag, and if it is found then a GFF3 file is created. If you suspect that files are not created for some genomes that should have them, then the NMPDR flag has not been set. The creation takes about 30-40 seconds per genome, so you can expect it to run for some time. Once complete you will have a directory structure that looks something like this (only the first two genomes are shown for each organism): *NMPDR **Campylobacter ***Campylobacter.coli.RM2228.gff3 ***Campylobacter.jejuni.subsp.jejuni.84-25.gff3 ***... **Listeria ***Listeria.innocua.Clip11262.gff3 ***Listeria.monocytogenes.EGD-e.gff3 ***... **Staphylococcus ***Staphylococcus.aureus.RF122.gff3 ***Staphylococcus.aureus.subsp.aureus.MRSA252.gff3 ***... **Streptococcus ***Streptococcus.pneumoniae.R6.gff3 ***Streptococcus.pyogenes.MGAS10270.gff3 ***... **Vibrio ***Vibrio.cholerae.MO10.gff3 ***Vibrio.cholerae.O395.gff3 ***... ===Uploading the files=== One the creation of the GFF3 files is complete, you need to use the [http://iowg.brcdevel.org/gff3validator/ brc-central validator] to validate and upload the data to the site. The one tricky thing about this was that it requires the GO::Parser PERL module. This should be part of the standard install everywhere now, but you may run into problems if it is missing. Please contact Bob for help. Use this command to validate and upload our data: gff3_validator.pl -b NMPDR -d /path/to/directory/NMPDR -p CDS One this has completed you should ftp to [ftp://ftp.brc-central.org] and check that the files are correct. If there are problems with the validator or upload you should email Todd Creasy at TIGR for help. 448ed45c0d7749c8118613175efe6e956eb93552 1589 1588 2006-11-14T14:43:59Z RobEdwards 14 /* How to Create and Release GFF3 files to the BRCs */ wikitext text/x-wiki == How to Create and Release GFF3 files to the BRCs == We regularly release our data to BRC-central via GFF3 files. This page describes the steps to release the data. ===Creating the files=== Choose a machine that is upto date, and create an empty directory. For this example, we'll use the directory NMPDR Run the command nmpdr2gff NMPDR This looks through all genomes for the NMPDR flag, and if it is found then a GFF3 file is created using the seed2gff command. If you suspect that files are not created for some genomes that should have them, then the NMPDR flag has not been set. If you would like to create a gff3 file of a single organism, you can use seed2gff with just that organism. The creation takes about 30-40 seconds per genome, so you can expect it to run for some time. Once complete you will have a directory structure that looks something like this (only the first two genomes are shown for each organism): *NMPDR **Campylobacter ***Campylobacter.coli.RM2228.gff3 ***Campylobacter.jejuni.subsp.jejuni.84-25.gff3 ***... **Listeria ***Listeria.innocua.Clip11262.gff3 ***Listeria.monocytogenes.EGD-e.gff3 ***... **Staphylococcus ***Staphylococcus.aureus.RF122.gff3 ***Staphylococcus.aureus.subsp.aureus.MRSA252.gff3 ***... **Streptococcus ***Streptococcus.pneumoniae.R6.gff3 ***Streptococcus.pyogenes.MGAS10270.gff3 ***... **Vibrio ***Vibrio.cholerae.MO10.gff3 ***Vibrio.cholerae.O395.gff3 ***... ===Uploading the files=== One the creation of the GFF3 files is complete, you need to use the [http://iowg.brcdevel.org/gff3validator/ brc-central validator] to validate and upload the data to the site. The one tricky thing about this was that it requires the GO::Parser PERL module. This should be part of the standard install everywhere now, but you may run into problems if it is missing. Please contact Bob for help. Use this command to validate and upload our data: gff3_validator.pl -b NMPDR -d /path/to/directory/NMPDR -p CDS One this has completed you should ftp to [ftp://ftp.brc-central.org] and check that the files are correct. If there are problems with the validator or upload you should email Todd Creasy at TIGR for help. f07a540ae89b84f9cf4e82328ce334f24304f07c 8 1090 1591 1496 2006-11-22T17:18:02Z FolkerMeyer 2 SEED Viewer is now available via the homepage wikitext text/x-wiki * navigation ** Home_of_the_SEED|Home of the SEED ** Annotating_1000_genomes|Manifesto ** SEED_People| SEED People ** Contact| Contact * SEEDs ** http://seed-viewer.theseed.org/|SEED-Viewer ** http://theseed.uchicago.edu/FIG/index.cgi|Trial-SEED ** http://seed.sdsu.edu/FIG/index.cgi|Metagenomics SEED * Miscellaneous ** DownloadPage|Download Page ** Glossary|Glossary ** SOPs|SOPs ** SpecialPurposeDBs|Special Purpose DBs 0e24a23ce3a75efc3c8d8836326b6c9e85f71c58 0 1374 1592 1512 2006-12-01T14:01:55Z WilliamMihalo 3 wikitext text/x-wiki The people behind SEED are the following: * [http://www.thefig.info FIG] ** Ross Overbeek ** Veronika Vonstein ** Gordon Pusch ** Bruce Parrello ** Rob Edwards ** Andrei Osterman ** Michael Fonstein ** Svetlana Gerdes ** Olga Zagnitko ** Olga Vassieva ** Yakov Kogan ** Irina Goltsman * [http://www.mcs.anl.gov Mathematics and Computer Science Department] [http://www.anl.gov Argonne National Labs] ** Rick Stevens ** Terry Disz ** Robert Olson ** Folker Meyer ** ... * [http://www.ci.uchicago.ed Computation Institute] [http://www.uchicago.edu University of Chicago] ** Daniela Bartels ** Matt Cohoon ** Kaitlyn Hwang ** Michael Kubal ** William Mihalo ** Daniel Paarmann ** Tobias Paczian ** Andreas Wilke ** Jen Zinner ** ... * [http://www.uiuc.edu University of Illinois at Urbana-Champaign] ** Gary J. Olson ** Leslie McNeil * [http://www.hope-college.edu Hope College] ** Matt DeJongh ** Aaron Best * [http://www.utmem.edu/ University of Memphis Tennessee] ** Rami Aziz 9a7d6b734d8271f8decd621197baf4c510c89c1a 1593 1592 2006-12-04T15:52:38Z FolkerMeyer 2 wikitext text/x-wiki The people behind SEED are the following: * [http://www.thefig.info FIG] ** Ross Overbeek ** Veronika Vonstein ** Gordon Pusch ** Bruce Parrello ** Rob Edwards ** Andrei Osterman ** Michael Fonstein ** Svetlana Gerdes ** Olga Zagnitko ** Olga Vassieva ** Yakov Kogan ** Irina Goltsman * [http://www.mcs.anl.gov Mathematics and Computer Science Department] [http://www.anl.gov Argonne National Labs] ** Rick Stevens ** Terry Disz ** Robert Olson ** Folker Meyer ** ... * [http://www.ci.uchicago.ed Computation Institute] [http://www.uchicago.edu University of Chicago] ** Daniela Bartels ** Matt Cohoon ** Kaitlyn Hwang ** Michael Kubal ** William Mihalo ** Daniel Paarmann ** Tobias Paczian ** Andreas Wilke ** Jen Zinner ** ... * [http://www.uiuc.edu University of Illinois at Urbana-Champaign] ** Gary J. Olson ** Leslie McNeil * [http://www.hope.edu Hope College] ** Matt DeJongh ** Aaron Best * [http://www.utmem.edu/ University of Memphis Tennessee] ** Rami Aziz d643aa8fab2f018587266e52f53b960c16bebe34 0 1379 1594 1482 2006-12-04T20:03:43Z FolkerMeyer 2 wikitext text/x-wiki == Annotation of Genomes: == === Standard Operating Procedure (FIG|SOP002)=== === Introduction === This procedure describes the annotation process used by the SEED and NMPDR annotators and curators. Let us begin by discussing a number of terms that we use in this document: '''Functional Role''': The concept of functional role is both basic and primitive in the sense that we will not pretend to offer a precise definition. It corresponds roughly to a single logical role that a gene or gene product may play in the operation of a cell. '''Gene function''': The function of a protein-encoding gene (PEG) is the functional role played by the product of the gene or an expression describing a set of roles played by the encoded protein. The operators used to construct expressions and the meanings associated with the operators are described in http://www.nmpdr.org/FIG/Html/SEED_functions.html Genes other than PEGs can also be assigned functions (e.g., SSU rRNA). However, in most cases the functions assigned to genes other than PEGs tend not to be problematic. This document will focus solely on annotation of PEGs. '''Assigning a gene function and annotation''': Annotators assign gene functions to genes, and we call this process annotation. In most contexts, people use the term annotation to refer to assignments of function to the genes within a single organism. We certainly use the term in this sense, but we also use it to describe the process of assigning functions to corresponding genes from numerous genomes. Our basic approach to annotation is to ask our annotators to annotate the genes included in a subsystem (e.g., glycolysis) across all genomes. This process of annotation of the genes within a subsystem across a set of genomes, rather than annotation of genes within a single genome, allows our annotators to focus on a constrained set of functional roles and attempt to accurately identify exactly what variant, if any, of a subsystem exists in each of the genomes. We use the term annotation to refer to assigning functions to genes (either within a single organism or to a constrained set of gene/protein families across a set of organisms). This activity certainly is closely related to the construction of subsystems and protein families (which we call FIGfams), but we will describe those activities elsewhere. '''Subsystem''': A subsystem is a set of functional roles that an annotator has decided should be thought of as related. Frequently, subsystems represent the collection of functional roles that make up a metabolic pathway, a complex (e.g., the ribosome), or a class of proteins (e.g., two-component signal-transduction proteins within Staphylococcus aureus). A populated subsystem is a subsystem with an attached spreadsheet. The rows of the spreadsheet represent genomes and the columns represent the functional roles of the spreadsheet. Each cell contains the identifiers of genes from the corresponding genome the implement the specific functional role. That is, a populated subsystem specifies which genes implement instances of the subsystem in each of the genomes. The rows of a populated genome are assigned variant codes which describe which of a set of possible variants of the subsystem exist within each genome (special codes expressing a total absence of the subsystem or remaining uncertainty exist). Construction of a large set of curated populated subsystems is at the center of the NMPDR and SEED annotation efforts. '''FIGfam''': FIGfams are protein families generated by the Fellowship for Interpretation of Genomes (FIG). These families are based on the collection of subsystems, as well as correspondences between genes in closely related strains (we describe the construction of FIGfams in a separate SOP). The important properties of these families are as follows: # Two PEGs which both occur within a single FIGfam are believed to have the same function. # There is a decision procedure associated with the family which can be invoked to determine whether or not a gene can be “safely” assigned the function associated with the family. '''Metabolic Reconstruction''': When we use the term metabolic reconstruction of a given genome we will simply mean the set of populated subsystems that contain the genome, the PEGs (and their assigned functions) that are connected to functional roles in these populated subsystems, and the specific variant code associated with the genome in each of the populated subsystems. '''NMPDR pathogen genome''': The NMPDR is responsible for five classes of genomes: # Campylobacter jejuni # Listeria monocytogenes # Staphylococcus aureus # Streptococcus pneumoniae and Streptococcus pyogenes # Pathogenic Vibrio We refer to these genomes as the NMPDR pathogens. The NMPDR carefully annotates some close relatives of these classes to provide accurate comparative context. Similarly, it includes a diverse collection of complete genomes that it annotates less accurately to provide context for comparative analysis. Now we can discuss what we mean by the annotations and the standard procedure for making those annotations. === The Annotation Procedure === The annotation of genomes begins after the genes have been identified and the genome has been integrated into a SEED environment. The annotation process then proceeds through the following steps: # Use of FIGfams # Use of Subsystems # Annotation of Prophages # Resolution of Conflicts # Improvement of Annotation Via New Subsystems # Continuous Refinement Via Analysis of Literature The following sections cover each of these steps in detail. We present the sequence of steps as commands issued from the command line. In fact, we are constructing a pipeline managed from a web interface that is intended to allow a relatively unskilled user to control the process. ==== Step 1: Use of FIGfams ==== For each new genome, we form a set of anticipated families by gathering all FIGfams with members in genomes from the same class. We begin the annotation by taking the anticipated families and searching for occurrences of these FIGfams within the new genome. This is achieved by invoking install_anticipated_functions User GenomeToBeAnnotated FileOfGenomesGivingContext Where User is the individual issuing the command, GenomeToBeAnnotated is the ID of the genome to be annotated (it is assumed that this genome has already been installed in the current SEED), and FileOfGenomesGivingContext is a file containing genome IDs (one per line) of the existing genomes from the same class. The effect of running this command will be to locate the instances of families when possible, to assign the appropriate function to the located genes, and to record detailed annotations of which FIGfam families were used as the basis for each annotation (along with the User and timestamps). ==== Step 2: Use of Subsystems ==== Once initial assignments based on FIGfams has been accomplished, it is possible to rapidly assess the presence and absence of subsystems (it is worth noting that every functional role within existing subsystems is covered by a FIGfam). The process begins with potentially_missed_assignments User GenomeToBeAnnotated FileOfGenomesGivingContext This command will produce a list of assignments that may have been missed. This list is formed by looking at subsystems contained in each of the genomes that make up the context, checking for subsystems in which a majority (but not all) of the genes have corresponding genes in the new genome, and candidates for the missing genes can be located. The tool produces a list of possibly missed assignments that must be checked by an annotator. The assignments are installed as an assignment set for the given User. Once the list of possibly missed assignments has been processed, the following command can be run: add_to_subsystems User GenomeToBeAnnotated FileOfGenomesGivingContext This command will compute the set of subsystems from the context genomes for which all of the corresponding genes can be located in the new genome. This set of subsystems will then be split into two lists: # Some of the subsystems are marked as automatically extendable by their curators. For these subsystems, the new genome will be added to the populated subsystem. # For those subsystems that are not marked as automatically extendable, the fact that the new genome should be added to the subsystem will be recorded. Curators for these subsystems will be notified and asked to add the new genome. The tentative metabolic reconstruction is formed (including subsystems from both lists). ==== Step 3: Resolution of Conflicts ==== FIGfams are not always annotated consistently. This can happen in cases in which it is possible to assert that a set of genes have a common function, but for which disagreement remains about exactly how to label the role played by members of the family. In such cases, a functional role is associated with the FIGfam, but individual members of the family may have distinct (inconsistent) functions. The number of such instances is gradually dropping, but we have adopted the position that it is better to retain the inconsistency (reflecting real uncertainty) rather than enforcing a common function. Execution of the following command will produce a list of conflicts that should be examined by an annotator: potential_conflicts GenomeToBeAnnotated FileOfGenomesGivingContext ==== Step 4: Improvement of Annotation Via New Subsystems ==== Normal subsystem maintenance occurs constantly. The basic activity of our annotators is to extend existing subsystems and to define and populate new subsystems. These activities produce a gradual improvement in the quality of annotations for all genomes. All new annotations are logged as they are made. ==== Step 5: Continuous Refinement Via Analysis of Literature ==== Annotators should continuously review new literature, seeking cases in which gene functions can be improved based on new results. Sometimes, this results in improvements in function for a specific gene (and these results are then propagated to other members of the NMPDR pathogen class). More often, these new results are used as the basis for new subsystems and have a broader impact. 9ea1806b35c77968b2a699c9745279003230d545 0 1378 1595 1436 2006-12-04T20:04:12Z FolkerMeyer 2 wikitext text/x-wiki Calling Genes: == Standard Operating Procedure (FIG|SOP001)== === Introduction === This procedure is designed to be used by members of the NMPDR and the SEED developers to call genes in two broad classes of genomes: • Genomes for NMPDR pathogens, which come from five sets of closely related strains of pathogens, and • Diverse genomes used to support comparative analysis. When we integrate diverse complete genomes, we often just take the genomes from RefSeq. Only in cases where the RefSeq gene calls require improvement do we apply similar procedures as for the NMPDR pathogens. This document describes the procedure used to call genes for NMPDR pathogens. === Summary of the procedure === The overall set of steps used to call genes is as follows: 1. Identify tRNAs: When we search for tRNAs in the diverse, non-NMPDR genomes, we use tRNAscan-SE, a tool developed by Sean Eddy, which we believe performs extremely well. However, for NMPDR pathogens, we maintain a library of all located tRNAs; locating the corresponding instances in new genomes is extremely straightforward. 2. Identify rRNAs: Again, for this we use a custom tool constructed by the NMPDR. Since the basic classes of rRNAs for each of the organisms curated by the NMPDR have been identified in several existing genomes, locating these rRNAs in new genomes is again completely straightforward. 3. Identify a set of expected genes: There is a set of “universal” genes and a number of families of highly conserved genes that are expected to be present in each of the NMPDR pathogens. We look for the genes candidates that are the most similar to these “universal” genes or matching the highly conserved gene families in each new genome, recording those instances that are found. 4. Use GLIMMER trained on the detected genes: We use the highly conserved gene candidates found in step (3.) as training set for GLIMMER 2, a tool developed and made available by TIGR. In most cases, we believe that the set of gene candidates identified by GLIMMER given a highly reliable training set (which we feel exist in the cases of NMPDR pathogens) should be a “superset” of the set of real genes (modulo a small rate of “false negatives”). 5. Resolve overlaps: We have developed a custom tool that resolves gene overlaps. Because we can use the gene-calls for a set of phylogenetically close organisms to validate the candidates gene calls in the new genome, we can reliably identify the vast majority of genes in steps 1--3 with high accuracy. Hence, we are confident that this overlap resolution tool performs well. 6. Backfill gaps: We check for potential short genes within any gaps exceeding 90 bp that remain after step 5. We do this by blasting the gaps between gene candidates against a collection of genomes from the immediate phylogenetic neighborhood (i.e., a fixed set of genomes for each of the general classes of NMPDR pathogens). Gene candidates that are detected are added to the calls from steps 1--5. In some cases, this step may add gene candidates that are not real; we therefore periodically review the calls in each set of close genomes for possible “false positives,” but in general, we would prefer to add a few too many genes, rather than leave out real ones. 7. Check Starts: A penultimate pass is made to adjust start positions using an algorithm based on seeking a consistent position in each of the sets of genomes curated by the NMPDR. The algorithm takes into account the start codon, the presence or absence of a ribosome binding site, and the ability to align candidate start positions with those in the existing set of close genomes. 8. Identification of potential frameshifts and pseudo-genes: As a last step, we run an automated tool that attempts to identify potential frameshifts and pseudo-genes. When these are detected, these features are recorded, along with the evidence supporting the assertion. Each of these steps generates a log entry summarizing the outcome. The final output constitutes a genome in a form that can be added to the SEED, and then into the NMPDR. === Details === ==== Step 1: Identify tRNAs ==== To locate the tRNAs and produce tbl/fasta entries, invoke find_instances –n User LibraryOfInstances SkeletalOrganismDirectory This tool assumes that the library contains instances of tRNAs from closely related genomes. It locates instances matching the tRNAs stored in the indicated library, updates the tbl and fasta file, adds corresponding assigned_functions entries, and logs the results. ==== Step 2: Identify rRNAs ==== To locate the tRNAs and produce tbl/fasta entries, invoke find_instances –n User LibraryOfInstances SkeletalOrganismDirectory This tool assumes that the library contains instances of rRNAs from closely related genomes. It locates instances matching the rRNAs stored in the indicated library, updates the tbl and fasta file, adds the corresponding assigned_functions entries, and logs the results. ==== Step 3: Identify a set of expected genes ==== The searching for and identifying protein-encoding genes is done in two steps: find_neighbors GenomeDirectory 20 found new > close.neighbors find_genes_based_on_neighbors GenomeDirectory found new < close.neighbors The first step takes DATA/FigFamsData and a genome directory (of the form xxxx.y) and locates the set of 20 closest genomes, calling a few genes in the process. The second command locates instances of of FIGfams that occur within the closely related genomes and in the new genome. In the case of closely-related NMPDR pathogens, we expect to locate 80-90% of the protein-encoding genes and to inherit annotations from existing genomes. ==== Step 4: Use GLIMMER trained on existing genes ==== The command recall_based_on_found GenomeDirectory close.neighbors > candidate_peg.tbl recalls the genes using GLIMMER, making sure that there is a gene for every protein-encoding gene (peg) that has already been called (with the same start). That is, this tool forms a superset of the previously called genes by merging the calls from a GLIMMER run trained using the existing set of protein-encoding gene-calls with the existing set. ==== Step 5: Resolve overlaps ==== By running resolve_overlaps GenomeDirectory candidate_peg.tbl we remove unacceptable overlaps between called genes and those determined by GLIMMER, and add them to the genes in GenomeDirectory. ==== Step 6: Backfill gaps ==== We then run backfill_gaps GenomeDirectory to search for possible genes in any gaps that appear to be unusually long. Here, we retain only genes that have similarity to genes that exist in other genomes (that are sufficiently distant from the new genome). ==== Step 7: Check Starts ==== We use adjust_starts GenomeDirectory to attempt to make starts consistent with those of genes in existing genomes. ==== Step 8: Identification of potential frameshifts and pseudo-genes ==== Finally, we run correct_frameshifts GenomeDirectory if we feel that we should attempt to automatically correct potential frameshifts. This will produce log entries documenting the “corrections”. If we prefer to simply add annotations to what appear to be fragments of genes (i.e., real pseudo-genes due to real frameshifts or partial genes due to assembly errors), we run instead annotate_potential_frameshifts GenomeDirectory which adds annotations describing the evidence for a potential frameshift. The decision to use one approach over the other is handled case by case. e5f12bb5c6b4cb82b177aaab849c3daddc7de270 6 1395 1603 2006-12-04T21:17:40Z WilliamMihalo 3 wikitext text/x-wiki da39a3ee5e6b4b0d3255bfef95601890afd80709 6 1397 1605 2006-12-04T21:28:49Z WilliamMihalo 3 A description of CentOS wikitext text/x-wiki A description of CentOS 13f7077fa54070eb09995992a503dd8943178d84 6 1398 1606 2006-12-04T21:39:34Z WilliamMihalo 3 listeria wikitext text/x-wiki listeria ada066c28ee2d8d2061dae932db610cf7d1cfda1 6 1399 1607 2006-12-04T21:43:22Z TerryDisz 4 wikitext text/x-wiki da39a3ee5e6b4b0d3255bfef95601890afd80709 6 1400 1608 2006-12-04T21:44:41Z TerryDisz 4 New Version wikitext text/x-wiki New Version add3bbbdbee187489026d61d825ccf84f644acff 6 1401 1609 2006-12-04T21:49:43Z TerryDisz 4 wikitext text/x-wiki da39a3ee5e6b4b0d3255bfef95601890afd80709 6 1402 1611 2006-12-06T14:20:23Z TerryDisz 4 wikitext text/x-wiki da39a3ee5e6b4b0d3255bfef95601890afd80709 6 1403 1613 2006-12-06T14:30:38Z TerryDisz 4 wikitext text/x-wiki da39a3ee5e6b4b0d3255bfef95601890afd80709 6 1404 1618 2006-12-06T14:44:10Z TerryDisz 4 wikitext text/x-wiki da39a3ee5e6b4b0d3255bfef95601890afd80709 0 1371 1619 1617 2006-12-06T14:46:04Z TerryDisz 4 wikitext text/x-wiki == SEED standard operating procedures == To generate data that is useful to the various communities involved in the process of annotation and use of annotations, we make available our standard operating procedures. * Annotation ** [[Image:The48hrserver.pdf]] Annotating a genome with the 48-hour service (NMPDR|SOP005) ** [[Image:GO AND PFAM SOP.pdf|thumb|Description]] Creation of GO-terms (NMPDR|SOP004) *BRC **[[Image:brc upload sop.pdf]] Releasing GFF3 files(NMPDR|SOP006) * Obsolete SOPs ** [[GeneCalling|Gene calling (NMPDR|SOP001)]] ** [[Annotation_of_close_strain_sets|Annotation of close strain sets(NMPDR|SOP002)]] ** [[Image:New_genome_sop.pdf]] Adding Genomes to the NMPDR (NMPDR|SOP003) ff2467045a6d00a5dbe2dba8063663640ee80fd4 1620 1619 2006-12-06T15:10:35Z TerryDisz 4 wikitext text/x-wiki == SEED standard operating procedures == To generate data that is useful to the various communities involved in the process of annotation and use of annotations, we make available our standard operating procedures. * Annotation ** Annotating a genome with the 48-hour service (NMPDR|SOP005) [[Image:The48hrserver.pdf]] ** Creation of GO-terms (NMPDR|SOP004) [[Image:GO AND PFAM SOP.pdf|thumb|Description]] *BRC **Releasing GFF3 files(NMPDR|SOP006) [[Image:brc upload sop.pdf]] * Obsolete SOPs ** [[GeneCalling|Gene calling (NMPDR|SOP001)]] ** [[Annotation_of_close_strain_sets|Annotation of close strain sets(NMPDR|SOP002)]] ** Adding Genomes to the NMPDR (NMPDR|SOP003) [[Image:New_genome_sop.pdf]] ce033992bd292a85aba41f8f683b1640369f9a7f 1622 1620 2006-12-06T15:27:30Z TerryDisz 4 wikitext text/x-wiki == SEED standard operating procedures == To generate data that is useful to the various communities involved in the process of annotation and use of annotations, we make available our standard operating procedures. * Annotation ** Annotation Codes (NMPDR|SOP010) [[Image:Annotation sop.pdf]] ** Annotating a genome with the 48-hour service (NMPDR|SOP005) [[Image:The48hrserver.pdf]] ** Creation of GO-terms (NMPDR|SOP004) [[Image:GO AND PFAM SOP.pdf|thumb|Description]] *BRC **Releasing GFF3 files(NMPDR|SOP006) [[Image:brc upload sop.pdf]] * Obsolete SOPs ** [[GeneCalling|Gene calling (NMPDR|SOP001)]] ** [[Annotation_of_close_strain_sets|Annotation of close strain sets(NMPDR|SOP002)]] ** Adding Genomes to the NMPDR (NMPDR|SOP003) [[Image:New_genome_sop.pdf]] 41f0ae13effc2015809993b65bbb92ffb3dcff71 6 1405 1621 2006-12-06T15:25:11Z TerryDisz 4 wikitext text/x-wiki da39a3ee5e6b4b0d3255bfef95601890afd80709 0 1 1623 1514 2006-12-11T17:11:11Z TerryDisz 4 fixed seed viewer link in body wikitext text/x-wiki With the growing number of available genomes, the need for an environment to support effective comparative analysis increases. The original SEED Project was started in 2003 by the [http://thefig.info Fellowship for Interpretation of Genomes (FIG)] as a largely unfunded open source effort. Argonne National Lab and the University of Chicago joined the project, and now much of the activity occurs at those two institutions (as well as the University of Illinois at Urbana-Champaign, Hope college, San Diego State University, the Burnham Institute and a number of other institutions). The cooperative effort focuses on the development of the comperative genomics environment called the SEED and, more importantly, on the development of curated genomic data. We provide a [http://seed-viewer.theseed.org/ SEED-Viewer] that allows read-only access to the latest curated data sets. For users interested in editing and learning how to use the system, we provide the [http://theseed.uchicago.edu/FIG/index.cgi Trial-SEED]. As described in our [[Annotating_1000_genomes|manifesto]] the [[Glossary#Annotation|annotation]] is not performed on a gene by gene basis per genome, but rather by [[Glossary#Subsystem|subsystem]] by an expert curator across many genomes at a time. We make all our software and data available for download and use on our [[DownloadPage]] page. * When using the SEED, please cite: Overbeek et al., [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16214803&query_hl=2&itool=pubmed_docsum|Nucleic Acids Res 33(17)], 2005 ([http://www.theseed.org/SubsystemPaperSupplementalMaterial/index.html Supplementary material]) * Our approaches to annotation, gene calling etc are outlined in a series of [[SOPs|Standard Operating Procedures]]. 6b8f7ac6789f1f6825504b62f3529d17552715e4 1624 1623 2007-02-05T22:12:05Z FolkerMeyer 2 wikitext text/x-wiki With the growing number of available genomes, the need for an environment to support effective comparative analysis increases. The original SEED Project was started in 2003 by the [http://thefig.info Fellowship for Interpretation of Genomes (FIG)] as a largely unfunded open source effort. Argonne National Lab and the University of Chicago joined the project, and now much of the activity occurs at those two institutions (as well as the University of Illinois at Urbana-Champaign, Hope college, San Diego State University, the Burnham Institute and a number of other institutions). The cooperative effort focuses on the development of the comparative genomics environment called the SEED and, more importantly, on the development of curated genomic data. We provide a [http://seed-viewer.theseed.org/ SEED-Viewer] that allows read-only access to the latest curated data sets. For users interested in editing and learning how to use the system, we provide the [http://theseed.uchicago.edu/FIG/index.cgi Trial-SEED]. As described in our [[Annotating_1000_genomes|manifesto]] the [[Glossary#Annotation|annotation]] is not performed on a gene by gene basis per genome, but rather by [[Glossary#Subsystem|subsystem]] by an expert curator across many genomes at a time. We make all our software and data available for download and use on our [[DownloadPage]] page. * When using the SEED, please cite: Overbeek et al., [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16214803&query_hl=2&itool=pubmed_docsum|Nucleic Acids Res 33(17)], 2005 ([http://www.theseed.org/SubsystemPaperSupplementalMaterial/index.html Supplementary material]) * Our approaches to annotation, gene calling etc are outlined in a series of [[SOPs|Standard Operating Procedures]]. 86a096e19aec9b2dcf6a547ba5b1785287900652 1631 1624 2007-05-21T17:48:51Z WilliamMihalo 3 wikitext text/x-wiki With the growing number of available genomes, the need for an environment to support effective comparative analysis increases. The original SEED Project was started in 2003 by the [http://thefig.info Fellowship for Interpretation of Genomes (FIG)] as a largely unfunded open source effort. Argonne National Lab and the University of Chicago joined the project, and now much of the activity occurs at those two institutions (as well as the University of Illinois at Urbana-Champaign, Hope college, San Diego State University, the Burnham Institute and a number of other institutions). The cooperative effort focuses on the development of the comparative genomics environment called the SEED and, more importantly, on the development of curated genomic data. We provide a [http://seed-viewer.theseed.org/ SEED-Viewer] that allows read-only access to the latest curated data sets. For users interested in editing and learning how to use the system, we provide the [http://theseed.uchicago.edu/FIG/index.cgi Trial-SEED]. As described in our [[Annotating_1000_genomes|manifesto]] the [[Glossary#Annotation|annotation]] is not performed on a gene by gene basis per genome, but rather by [[Glossary#Subsystem|subsystem]] by an expert curator across many genomes at a time. We make all our software and data available for download and use on our [[DownloadPage]] page. * When using the SEED, please cite: Overbeek et al., [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16214803&query_hl=2&itool=pubmed_docsum|Nucleic Acids Res 33(17)], 2005 ([http://www.theseed.org/SubsystemPaperSupplementalMaterial/index.html Supplementary material]) * Our approaches to annotation, gene calling etc are outlined in a series of [[SOPs|Standard Operating Procedures]]. f6b7bc549ef1de19389e095a342a01101d29c001 1666 1631 2007-07-04T15:13:14Z WilliamMihalo 3 wikitext text/x-wiki With the growing number of available genomes, the need for an environment to support effective comparative analysis increases. The original SEED Project was started in 2003 by the [http://thefig.info Fellowship for Interpretation of Genomes (FIG)] as a largely unfunded open source effort. Argonne National Lab and the University of Chicago joined the project, and now much of the activity occurs at those two institutions (as well as the University of Illinois at Urbana-Champaign, Hope college, San Diego State University, the Burnham Institute and a number of other institutions). The cooperative effort focuses on the development of the comparative genomics environment called the SEED and, more importantly, on the development of curated genomic data. We provide a [http://seed-viewer.theseed.org/ SEED-Viewer] that allows read-only access to the latest curated data sets. For users interested in editing and learning how to use the system, we provide the [http://theseed.uchicago.edu/FIG/index.cgi Trial-SEED]. As described in our [[Annotating_1000_genomes|manifesto]] the [[Glossary#Annotation|annotation]] is not performed on a gene by gene basis per genome, but rather by [[Glossary#Subsystem|subsystem]] by an expert curator across many genomes at a time. We make all our software and data available for download and use on our [[DownloadPage]] page. * When using the SEED, please cite: Overbeek et al., [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16214803&query_hl=2&itool=pubmed_docsum|Nucleic Acids Res 33(17)], 2005 ([http://www.theseed.org/SubsystemPaperSupplementalMaterial/index.html Supplementary material]) * Our approaches to annotation, gene calling etc are outlined in a series of [[SOPs|Standard Operating Procedures]]. 9ef4ee0b2f85db946add81555d6dd1ded3472a8a 0 1367 1625 1511 2007-03-01T21:26:10Z FolkerMeyer 2 Include the Linking to SEED list of supported external Identifiers wikitext text/x-wiki === Annotators SEED === The master copy for all data in the SEED environment. Users can not access this password protected site. All annotations are made available via the [[#SEED-Viewer| SEED-Viewer]] and the [[#Trial-SEED|Trial-SEED]]. === Annotation === please see [[#Assigning_a_gene_function_and_annotation| Assigning a gene function and annotation]] === Assigning a gene function and annotation === Annotators assign gene functions to genes, and we call this process annotation. In most contexts, people use the term annotation to refer to assignments of function to the genes within a single organism. We certainly use the term in this sense, but we also use it to describe the process of assigning functions to corresponding genes from numerous genomes. Our basic approach to annotation is to ask our annotators to annotate the genes included in a [[#subsystem|Subsystem]] (e.g., glycolysis) across all genomes. This process of annotation of the genes within a subsystem across a set of genomes, rather than annotation of genes within a single genome, allows our annotators to focus on a constrained set of functional roles and attempt to accurately identify exactly what variant, if any, of a subsystem exists in each of the genomes. We use the term annotation to refer to assigning functions to genes (either within a single organism or to a constrained set of gene/protein families across a set of organisms). This activity certainly is closely related to the construction of subsystems and protein families (which we call FIGfams), but we will describe those activities elsewhere. === Assignment === please see [[#Assigning_a_gene_function_and_annotation| Assigning a gene function and annotation]] === Bidirectional Best Hit (BBH) === The paper [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=EBI&pubmedid=10077608 The use of gene clusters to infer functional coupling] defines a Bidirectional Best Hit or BBH as follows: <blockquote> Given two genes Xa and Xb from two genomes Ga and Gb, Xa and Xb are called a “bidirectional best hit (BBH)” if and only if recognizable similarity exists between them (in our case, we required fasta3 scores lower than 1.0 × 10−5), there is no gene Zb in Gb that is more similar than Xb is to Xa, and there is no gene Za in Ga that is more similar than Xa is to Xb. Genes (Xa, Ya) from Ga and (Xb, Yb) from Gb form a “pair of close bidirectional best hits (PCBBH)” if and only if Xa and Ya are close, Xb and Yb are close, Xa and Xb are a BBH, and Ya and Yb are a BBH. </blockquote> === Clearinghouse === please see [[#SubsystemClearinghouse|Subsystem Clearinghouse]] ===Feature=== A feature is a defined region in the DNA. A PEG is the most prevalent feature type in the SEED. Some other feature types include RNA, prophage and pathogenicity islands. The format for a feature ID is fig|genome_id.feature_abbreviation.feature_number (ie fig|83333.1.peg.100 ). === FIGfam === FIGfams are protein families generated by the Fellowship for Interpretation of Genomes (FIG). These families are based on the collection of subsystems, as well as correspondences between genes in closely related strains (we describe the construction of FIGfams in a separate SOP). The important properties of these families are as follows: # Two PEGs which both occur within a single FIGfam are believed to have the same function. # There is a decision procedure associated with the family which can be invoked to determine whether or not a gene can be “safely” assigned the function associated with the family. === Functional role === The concept of functional role is both basic and primitive in the sense that we will not pretend to offer a precise definition. It corresponds roughly to a single logical role that a gene or gene product may play in the operation of a cell. === Gene function === The function of a protein-encoding gene (PEG) is the functional role played by the product of the gene or an expression describing a set of roles played by the encoded protein. The operators used to construct expressions and the meanings associated with the operators are described in http://www.nmpdr.org/FIG/Html/SEED_functions.html Genes other than PEGs can also be assigned functions (e.g., SSU rRNA). However, in most cases the functions assigned to genes other than PEGs tend not to be problematic. === Linking to the SEED === We support linking to the SEED via our supported identifiers: {| |+ Supported SEED Identifiers for external use ! Entity type !! key !! identifier !! Example |- | Genome || genome || fig<nowiki>|</nowiki>83331.1 || [[http://www.theseed.org/linkin.cgi?genome=fig|83331.1 http://www.theseed.org/linkin.cgi?genome=fig&#124;83331.1]] |- | PEG || id || fig<nowiki>|</nowiki>83331.peg.123 || [[http://seed-viewer.theseed.org/linkin.cgi?id=fig|83331.1.peg.123 http://seed-viewer.theseed.org/linkin.cgi?id=fig&#124;83331.1.peg.123]] |- | RNA feature || id || fig<nowiki>|</nowiki>83331.rna.1 || [[http://seed-viewer.theseed.org/linkin.cgi?id=fig|83331.1.rna.1 http://seed-viewer.theseed.org/linkin.cgi?id=fig&#124;83331.1.rna.1]] |- |} === Metabolic Reconstruction === When we use the term metabolic reconstruction of a given genome we will simply mean the set of populated subsystems that contain the genome, the PEGs (and their assigned functions) that are connected to functional roles in these populated subsystems, and the specific variant code associated with the genome in each of the populated subsystems. === NMPDR pathogen genome === The NMPDR is responsible for five classes of genomes: # Campylobacter jejuni # Listeria monocytogenes # Staphylococcus aureus # Streptococcus pneumoniae and Streptococcus pyogenes # Pathogenic Vibrio === Pair of Close Homologs (PCH) === The paper [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=EBI&pubmedid=10077608 The use of gene clusters to infer functional coupling] defines a Pair of Close Homologs as follows: <blockquote> We can also define the concept of “pairs of close homologs” (PCHs) as follows: genes (X′a, Y′a) from Ga and (X′b, Y′b) from Gb form a PCH if and only if X′a and Y′a are close, X′b and Y′b are close, X′a and X′b are recognizably similar, and Y′a and Y′b are recognizably similar. Here, we will consider two genes to be recognizably similar if their gene products produce fasta3 scores lower than 1.0 × 10−5. We use a scoring scheme analogous to the one described for PCBBHs to evaluate the connections between PCHs, except that if Ga and Gb are the same genome, we assign an arbitrary “same-genome score” (“same-genome” pairs cannot occur for PCBBHs by definition, but for PCHs they are possible). Unlike PCBBHs from two very close genomes for which contiguity is completely uninformative in the vast majority of cases, PCHs allow recognition of gene clusters that play similar (but usually not identical) roles (such as two transport cassettes containing pairs of homologs) in the same or similar organisms. The arbitrary “same-genome score” should, we believe, have a value that is high enough to rank such instances as significant. </blockquote> === PEG === A Protein Encoding Gene (PEG) is equivalent to a CDS (Coding Sequence). === Populated Subsystem === please see [[#Subsystem|Subsystem]] === SEED-Viewer === A read-only version of the SEED that presents the latest data. http://seed-viewer.theseed.org '''Please note''': The data is updated automatically every 24 hours. When citing or linking to the SEED please use this version. === Subsystem === A subsystem is a set of functional roles that an annotator has decided should be thought of as related. Frequently, subsystems represent the collection of [[#Functional_role|functional roles]] that make up a metabolic pathway, a complex (e.g., the ribosome), or a class of proteins (e.g., two-component signal-transduction proteins within Staphylococcus aureus). A '''populated subsystem''' is a subsystem with an attached spreadsheet. The rows of the spreadsheet represent genomes and the columns represent the functional roles of the spreadsheet. Each cell contains the identifiers of genes from the corresponding genome the implement the specific functional role. That is, a populated subsystem specifies which genes implement instances of the subsystem in each of the genomes. The rows of a populated genome are assigned '''variant codes''' which describe which of a set of possible variants of the subsystem exist within each genome (special codes expressing a total absence of the subsystem or remaining uncertainty exist). Construction of a large set of curated populated subsystems is at the center of the NMPDR and SEED annotation efforts. === Subsystem Clearing House === Since annotators can work on any machine (including the public SEED) the way to propagate subsystems is via http://clearinghouse.theseed.org/clearinghouse_browser.cgi? === Trial-SEED === A public, read-write copy of the SEED is made available on http://theseed.uchicago.edu/FIG/index.cgi '''Please note''': The data on this server is updated in irregular intervals. Users should not assume that annotations made on this system will persist. Please publish your annotations to the [[#Subsystem_clearing_house|Subsystem Clearing house]]. === Variant Code=== please see [[#Subsystem|Subsystem]] f9df0e82fe3035d534a26d6238f6ebfd5a19e6de 1626 1625 2007-03-01T21:31:09Z FolkerMeyer 2 wikitext text/x-wiki === Annotators SEED === The master copy for all data in the SEED environment. Users can not access this password protected site. All annotations are made available via the [[#SEED-Viewer| SEED-Viewer]] and the [[#Trial-SEED|Trial-SEED]]. === Annotation === please see [[#Assigning_a_gene_function_and_annotation| Assigning a gene function and annotation]] === Assigning a gene function and annotation === Annotators assign gene functions to genes, and we call this process annotation. In most contexts, people use the term annotation to refer to assignments of function to the genes within a single organism. We certainly use the term in this sense, but we also use it to describe the process of assigning functions to corresponding genes from numerous genomes. Our basic approach to annotation is to ask our annotators to annotate the genes included in a [[#subsystem|Subsystem]] (e.g., glycolysis) across all genomes. This process of annotation of the genes within a subsystem across a set of genomes, rather than annotation of genes within a single genome, allows our annotators to focus on a constrained set of functional roles and attempt to accurately identify exactly what variant, if any, of a subsystem exists in each of the genomes. We use the term annotation to refer to assigning functions to genes (either within a single organism or to a constrained set of gene/protein families across a set of organisms). This activity certainly is closely related to the construction of subsystems and protein families (which we call FIGfams), but we will describe those activities elsewhere. === Assignment === please see [[#Assigning_a_gene_function_and_annotation| Assigning a gene function and annotation]] === Bidirectional Best Hit (BBH) === The paper [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=EBI&pubmedid=10077608 The use of gene clusters to infer functional coupling] defines a Bidirectional Best Hit or BBH as follows: <blockquote> Given two genes Xa and Xb from two genomes Ga and Gb, Xa and Xb are called a “bidirectional best hit (BBH)” if and only if recognizable similarity exists between them (in our case, we required fasta3 scores lower than 1.0 × 10−5), there is no gene Zb in Gb that is more similar than Xb is to Xa, and there is no gene Za in Ga that is more similar than Xa is to Xb. Genes (Xa, Ya) from Ga and (Xb, Yb) from Gb form a “pair of close bidirectional best hits (PCBBH)” if and only if Xa and Ya are close, Xb and Yb are close, Xa and Xb are a BBH, and Ya and Yb are a BBH. </blockquote> === Clearinghouse === please see [[#SubsystemClearinghouse|Subsystem Clearinghouse]] ===Feature=== A feature is a defined region in the DNA. A PEG is the most prevalent feature type in the SEED. Some other feature types include RNA, prophage and pathogenicity islands. The format for a feature ID is fig|genome_id.feature_abbreviation.feature_number (ie fig|83333.1.peg.100 ). === FIGfam === FIGfams are protein families generated by the Fellowship for Interpretation of Genomes (FIG). These families are based on the collection of subsystems, as well as correspondences between genes in closely related strains (we describe the construction of FIGfams in a separate SOP). The important properties of these families are as follows: # Two PEGs which both occur within a single FIGfam are believed to have the same function. # There is a decision procedure associated with the family which can be invoked to determine whether or not a gene can be “safely” assigned the function associated with the family. === Functional role === The concept of functional role is both basic and primitive in the sense that we will not pretend to offer a precise definition. It corresponds roughly to a single logical role that a gene or gene product may play in the operation of a cell. === Gene function === The function of a protein-encoding gene (PEG) is the functional role played by the product of the gene or an expression describing a set of roles played by the encoded protein. The operators used to construct expressions and the meanings associated with the operators are described in http://www.nmpdr.org/FIG/Html/SEED_functions.html Genes other than PEGs can also be assigned functions (e.g., SSU rRNA). However, in most cases the functions assigned to genes other than PEGs tend not to be problematic. === Linking to the SEED === We support linking to the SEED using a generic mechanism: {| |+ Supported SEED Identifiers for external use ! Entity type !! key !! identifier !! Example |- | Genome || genome || fig<nowiki>|</nowiki>83331.1 || [[http://www.theseed.org/linkin.cgi?genome=fig|83331.1 http://www.theseed.org/linkin.cgi?genome=fig&#124;83331.1]] |- | PEG || id || fig<nowiki>|</nowiki>83331.peg.123 || [[http://seed-viewer.theseed.org/linkin.cgi?id=fig|83331.1.peg.123 http://seed-viewer.theseed.org/linkin.cgi?id=fig&#124;83331.1.peg.123]] |- | RNA feature || id || fig<nowiki>|</nowiki>83331.rna.1 || [[http://seed-viewer.theseed.org/linkin.cgi?id=fig|83331.1.rna.1 http://seed-viewer.theseed.org/linkin.cgi?id=fig&#124;83331.1.rna.1]] |- |} SEED identifiers contain the NCBI taxonomy ID, thus if the taxonomy ID changes, we need to update our internal data accordingly. To provide stable external identifiers, we keep a list of IDs that have changed and display warning message informing the user of the change and provide a link to the new version of the data requested. === Metabolic Reconstruction === When we use the term metabolic reconstruction of a given genome we will simply mean the set of populated subsystems that contain the genome, the PEGs (and their assigned functions) that are connected to functional roles in these populated subsystems, and the specific variant code associated with the genome in each of the populated subsystems. === NMPDR pathogen genome === The NMPDR is responsible for five classes of genomes: # Campylobacter jejuni # Listeria monocytogenes # Staphylococcus aureus # Streptococcus pneumoniae and Streptococcus pyogenes # Pathogenic Vibrio === Pair of Close Homologs (PCH) === The paper [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=EBI&pubmedid=10077608 The use of gene clusters to infer functional coupling] defines a Pair of Close Homologs as follows: <blockquote> We can also define the concept of “pairs of close homologs” (PCHs) as follows: genes (X′a, Y′a) from Ga and (X′b, Y′b) from Gb form a PCH if and only if X′a and Y′a are close, X′b and Y′b are close, X′a and X′b are recognizably similar, and Y′a and Y′b are recognizably similar. Here, we will consider two genes to be recognizably similar if their gene products produce fasta3 scores lower than 1.0 × 10−5. We use a scoring scheme analogous to the one described for PCBBHs to evaluate the connections between PCHs, except that if Ga and Gb are the same genome, we assign an arbitrary “same-genome score” (“same-genome” pairs cannot occur for PCBBHs by definition, but for PCHs they are possible). Unlike PCBBHs from two very close genomes for which contiguity is completely uninformative in the vast majority of cases, PCHs allow recognition of gene clusters that play similar (but usually not identical) roles (such as two transport cassettes containing pairs of homologs) in the same or similar organisms. The arbitrary “same-genome score” should, we believe, have a value that is high enough to rank such instances as significant. </blockquote> === PEG === A Protein Encoding Gene (PEG) is equivalent to a CDS (Coding Sequence). === Populated Subsystem === please see [[#Subsystem|Subsystem]] === SEED-Viewer === A read-only version of the SEED that presents the latest data. http://seed-viewer.theseed.org '''Please note''': The data is updated automatically every 24 hours. When citing or linking to the SEED please use this version. === Subsystem === A subsystem is a set of functional roles that an annotator has decided should be thought of as related. Frequently, subsystems represent the collection of [[#Functional_role|functional roles]] that make up a metabolic pathway, a complex (e.g., the ribosome), or a class of proteins (e.g., two-component signal-transduction proteins within Staphylococcus aureus). A '''populated subsystem''' is a subsystem with an attached spreadsheet. The rows of the spreadsheet represent genomes and the columns represent the functional roles of the spreadsheet. Each cell contains the identifiers of genes from the corresponding genome the implement the specific functional role. That is, a populated subsystem specifies which genes implement instances of the subsystem in each of the genomes. The rows of a populated genome are assigned '''variant codes''' which describe which of a set of possible variants of the subsystem exist within each genome (special codes expressing a total absence of the subsystem or remaining uncertainty exist). Construction of a large set of curated populated subsystems is at the center of the NMPDR and SEED annotation efforts. === Subsystem Clearing House === Since annotators can work on any machine (including the public SEED) the way to propagate subsystems is via http://clearinghouse.theseed.org/clearinghouse_browser.cgi? === Trial-SEED === A public, read-write copy of the SEED is made available on http://theseed.uchicago.edu/FIG/index.cgi '''Please note''': The data on this server is updated in irregular intervals. Users should not assume that annotations made on this system will persist. Please publish your annotations to the [[#Subsystem_clearing_house|Subsystem Clearing house]]. === Variant Code=== please see [[#Subsystem|Subsystem]] a6eb46ce74df001559ff1e71caea150ce36deac9 1627 1626 2007-03-02T21:47:23Z FolkerMeyer 2 wikitext text/x-wiki === Annotators SEED === The master copy for all data in the SEED environment. Users can not access this password protected site. All annotations are made available via the [[#SEED-Viewer| SEED-Viewer]] and the [[#Trial-SEED|Trial-SEED]]. === Annotation === please see [[#Assigning_a_gene_function_and_annotation| Assigning a gene function and annotation]] === Assigning a gene function and annotation === Annotators assign gene functions to genes, and we call this process annotation. In most contexts, people use the term annotation to refer to assignments of function to the genes within a single organism. We certainly use the term in this sense, but we also use it to describe the process of assigning functions to corresponding genes from numerous genomes. Our basic approach to annotation is to ask our annotators to annotate the genes included in a [[#subsystem|Subsystem]] (e.g., glycolysis) across all genomes. This process of annotation of the genes within a subsystem across a set of genomes, rather than annotation of genes within a single genome, allows our annotators to focus on a constrained set of functional roles and attempt to accurately identify exactly what variant, if any, of a subsystem exists in each of the genomes. We use the term annotation to refer to assigning functions to genes (either within a single organism or to a constrained set of gene/protein families across a set of organisms). This activity certainly is closely related to the construction of subsystems and protein families (which we call FIGfams), but we will describe those activities elsewhere. === Assignment === please see [[#Assigning_a_gene_function_and_annotation| Assigning a gene function and annotation]] === Bidirectional Best Hit (BBH) === The paper [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=EBI&pubmedid=10077608 The use of gene clusters to infer functional coupling] defines a Bidirectional Best Hit or BBH as follows: <blockquote> Given two genes Xa and Xb from two genomes Ga and Gb, Xa and Xb are called a “bidirectional best hit (BBH)” if and only if recognizable similarity exists between them (in our case, we required fasta3 scores lower than 1.0 × 10−5), there is no gene Zb in Gb that is more similar than Xb is to Xa, and there is no gene Za in Ga that is more similar than Xa is to Xb. Genes (Xa, Ya) from Ga and (Xb, Yb) from Gb form a “pair of close bidirectional best hits (PCBBH)” if and only if Xa and Ya are close, Xb and Yb are close, Xa and Xb are a BBH, and Ya and Yb are a BBH. </blockquote> === Clearinghouse === please see [[#SubsystemClearinghouse|Subsystem Clearinghouse]] ===Feature=== A feature is a defined region in the DNA. A PEG is the most prevalent feature type in the SEED. Some other feature types include RNA, prophage and pathogenicity islands. The format for a feature ID is fig|genome_id.feature_abbreviation.feature_number (ie fig|83333.1.peg.100 ). === FIGfam === FIGfams are protein families generated by the Fellowship for Interpretation of Genomes (FIG). These families are based on the collection of subsystems, as well as correspondences between genes in closely related strains (we describe the construction of FIGfams in a separate SOP). The important properties of these families are as follows: # Two PEGs which both occur within a single FIGfam are believed to have the same function. # There is a decision procedure associated with the family which can be invoked to determine whether or not a gene can be “safely” assigned the function associated with the family. === Functional role === The concept of functional role is both basic and primitive in the sense that we will not pretend to offer a precise definition. It corresponds roughly to a single logical role that a gene or gene product may play in the operation of a cell. === Gene function === The function of a protein-encoding gene (PEG) is the functional role played by the product of the gene or an expression describing a set of roles played by the encoded protein. The operators used to construct expressions and the meanings associated with the operators are described in http://www.nmpdr.org/FIG/Html/SEED_functions.html Genes other than PEGs can also be assigned functions (e.g., SSU rRNA). However, in most cases the functions assigned to genes other than PEGs tend not to be problematic. === Linking to the SEED === We support linking to the SEED using a generic mechanism: {| |+ Supported SEED Identifiers for external use ! Entity type !! key !! identifier !! Example |- | Genome || genome || fig<nowiki>|</nowiki>83331.1 || [[http://www.theseed.org/linkin.cgi?genome=fig|83333.1 http://www.theseed.org/linkin.cgi?genome=fig&#124;83333.1]] |- | PEG || id || fig<nowiki>|</nowiki>83331.peg.123 || [[http://seed-viewer.theseed.org/linkin.cgi?id=fig|83333.1.peg.123 http://seed-viewer.theseed.org/linkin.cgi?id=fig&#124;83333.1.peg.123]] |- | RNA feature || id || fig<nowiki>|</nowiki>83331.rna.1 || [[http://seed-viewer.theseed.org/linkin.cgi?id=fig|83333.1.rna.1 http://seed-viewer.theseed.org/linkin.cgi?id=fig&#124;83333.1.rna.1]] |- |} SEED identifiers contain the NCBI taxonomy ID, thus if the taxonomy ID changes, we need to update our internal data accordingly. To provide stable external identifiers, we keep a list of IDs that have changed and display warning message informing the user of the change and provide a link to the new version of the data requested. === Metabolic Reconstruction === When we use the term metabolic reconstruction of a given genome we will simply mean the set of populated subsystems that contain the genome, the PEGs (and their assigned functions) that are connected to functional roles in these populated subsystems, and the specific variant code associated with the genome in each of the populated subsystems. === NMPDR pathogen genome === The NMPDR is responsible for five classes of genomes: # Campylobacter jejuni # Listeria monocytogenes # Staphylococcus aureus # Streptococcus pneumoniae and Streptococcus pyogenes # Pathogenic Vibrio === Pair of Close Homologs (PCH) === The paper [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=EBI&pubmedid=10077608 The use of gene clusters to infer functional coupling] defines a Pair of Close Homologs as follows: <blockquote> We can also define the concept of “pairs of close homologs” (PCHs) as follows: genes (X′a, Y′a) from Ga and (X′b, Y′b) from Gb form a PCH if and only if X′a and Y′a are close, X′b and Y′b are close, X′a and X′b are recognizably similar, and Y′a and Y′b are recognizably similar. Here, we will consider two genes to be recognizably similar if their gene products produce fasta3 scores lower than 1.0 × 10−5. We use a scoring scheme analogous to the one described for PCBBHs to evaluate the connections between PCHs, except that if Ga and Gb are the same genome, we assign an arbitrary “same-genome score” (“same-genome” pairs cannot occur for PCBBHs by definition, but for PCHs they are possible). Unlike PCBBHs from two very close genomes for which contiguity is completely uninformative in the vast majority of cases, PCHs allow recognition of gene clusters that play similar (but usually not identical) roles (such as two transport cassettes containing pairs of homologs) in the same or similar organisms. The arbitrary “same-genome score” should, we believe, have a value that is high enough to rank such instances as significant. </blockquote> === PEG === A Protein Encoding Gene (PEG) is equivalent to a CDS (Coding Sequence). === Populated Subsystem === please see [[#Subsystem|Subsystem]] === SEED-Viewer === A read-only version of the SEED that presents the latest data. http://seed-viewer.theseed.org '''Please note''': The data is updated automatically every 24 hours. When citing or linking to the SEED please use this version. === Subsystem === A subsystem is a set of functional roles that an annotator has decided should be thought of as related. Frequently, subsystems represent the collection of [[#Functional_role|functional roles]] that make up a metabolic pathway, a complex (e.g., the ribosome), or a class of proteins (e.g., two-component signal-transduction proteins within Staphylococcus aureus). A '''populated subsystem''' is a subsystem with an attached spreadsheet. The rows of the spreadsheet represent genomes and the columns represent the functional roles of the spreadsheet. Each cell contains the identifiers of genes from the corresponding genome the implement the specific functional role. That is, a populated subsystem specifies which genes implement instances of the subsystem in each of the genomes. The rows of a populated genome are assigned '''variant codes''' which describe which of a set of possible variants of the subsystem exist within each genome (special codes expressing a total absence of the subsystem or remaining uncertainty exist). Construction of a large set of curated populated subsystems is at the center of the NMPDR and SEED annotation efforts. === Subsystem Clearing House === Since annotators can work on any machine (including the public SEED) the way to propagate subsystems is via http://clearinghouse.theseed.org/clearinghouse_browser.cgi? === Trial-SEED === A public, read-write copy of the SEED is made available on http://theseed.uchicago.edu/FIG/index.cgi '''Please note''': The data on this server is updated in irregular intervals. Users should not assume that annotations made on this system will persist. Please publish your annotations to the [[#Subsystem_clearing_house|Subsystem Clearing house]]. === Variant Code=== please see [[#Subsystem|Subsystem]] 10786b1194f74c0fd3a121adbebc48b4f50e35da 1629 1627 2007-04-20T14:50:44Z FolkerMeyer 2 /* Linking to the SEED */ wikitext text/x-wiki === Annotators SEED === The master copy for all data in the SEED environment. Users can not access this password protected site. All annotations are made available via the [[#SEED-Viewer| SEED-Viewer]] and the [[#Trial-SEED|Trial-SEED]]. === Annotation === please see [[#Assigning_a_gene_function_and_annotation| Assigning a gene function and annotation]] === Assigning a gene function and annotation === Annotators assign gene functions to genes, and we call this process annotation. In most contexts, people use the term annotation to refer to assignments of function to the genes within a single organism. We certainly use the term in this sense, but we also use it to describe the process of assigning functions to corresponding genes from numerous genomes. Our basic approach to annotation is to ask our annotators to annotate the genes included in a [[#subsystem|Subsystem]] (e.g., glycolysis) across all genomes. This process of annotation of the genes within a subsystem across a set of genomes, rather than annotation of genes within a single genome, allows our annotators to focus on a constrained set of functional roles and attempt to accurately identify exactly what variant, if any, of a subsystem exists in each of the genomes. We use the term annotation to refer to assigning functions to genes (either within a single organism or to a constrained set of gene/protein families across a set of organisms). This activity certainly is closely related to the construction of subsystems and protein families (which we call FIGfams), but we will describe those activities elsewhere. === Assignment === please see [[#Assigning_a_gene_function_and_annotation| Assigning a gene function and annotation]] === Bidirectional Best Hit (BBH) === The paper [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=EBI&pubmedid=10077608 The use of gene clusters to infer functional coupling] defines a Bidirectional Best Hit or BBH as follows: <blockquote> Given two genes Xa and Xb from two genomes Ga and Gb, Xa and Xb are called a “bidirectional best hit (BBH)” if and only if recognizable similarity exists between them (in our case, we required fasta3 scores lower than 1.0 × 10−5), there is no gene Zb in Gb that is more similar than Xb is to Xa, and there is no gene Za in Ga that is more similar than Xa is to Xb. Genes (Xa, Ya) from Ga and (Xb, Yb) from Gb form a “pair of close bidirectional best hits (PCBBH)” if and only if Xa and Ya are close, Xb and Yb are close, Xa and Xb are a BBH, and Ya and Yb are a BBH. </blockquote> === Clearinghouse === please see [[#SubsystemClearinghouse|Subsystem Clearinghouse]] ===Feature=== A feature is a defined region in the DNA. A PEG is the most prevalent feature type in the SEED. Some other feature types include RNA, prophage and pathogenicity islands. The format for a feature ID is fig|genome_id.feature_abbreviation.feature_number (ie fig|83333.1.peg.100 ). === FIGfam === FIGfams are protein families generated by the Fellowship for Interpretation of Genomes (FIG). These families are based on the collection of subsystems, as well as correspondences between genes in closely related strains (we describe the construction of FIGfams in a separate SOP). The important properties of these families are as follows: # Two PEGs which both occur within a single FIGfam are believed to have the same function. # There is a decision procedure associated with the family which can be invoked to determine whether or not a gene can be “safely” assigned the function associated with the family. === Functional role === The concept of functional role is both basic and primitive in the sense that we will not pretend to offer a precise definition. It corresponds roughly to a single logical role that a gene or gene product may play in the operation of a cell. === Gene function === The function of a protein-encoding gene (PEG) is the functional role played by the product of the gene or an expression describing a set of roles played by the encoded protein. The operators used to construct expressions and the meanings associated with the operators are described in http://www.nmpdr.org/FIG/Html/SEED_functions.html Genes other than PEGs can also be assigned functions (e.g., SSU rRNA). However, in most cases the functions assigned to genes other than PEGs tend not to be problematic. === Linking to the SEED === We support linking to the SEED using a generic mechanism: Base URL: http://www.theseed.org/linkin.cgi? {| |+ Supported SEED Identifiers for external use ! Entity type !! key !! identifier !! Example |- | Genome || genome || fig<nowiki>|</nowiki>83331.1 || [[http://www.theseed.org/linkin.cgi?genome=fig|83333.1 http://www.theseed.org/linkin.cgi?genome=fig&#124;83333.1]] |- | PEG || id || fig<nowiki>|</nowiki>83331.peg.123 || [[http://www.theseed.org/linkin.cgi?id=fig|83333.1.peg.123 http://seed-viewer.theseed.org/linkin.cgi?id=fig&#124;83333.1.peg.123]] |- | RNA feature || id || fig<nowiki>|</nowiki>83331.rna.1 || [[http://www.theseed.org/linkin.cgi?id=fig|83333.1.rna.1 http://seed-viewer.theseed.org/linkin.cgi?id=fig&#124;83333.1.rna.1]] |- |} SEED identifiers contain the NCBI taxonomy ID, thus if the taxonomy ID changes, we need to update our internal data accordingly. To provide stable external identifiers, we keep a list of IDs that have changed and display warning message informing the user of the change and provide a link to the new version of the data requested. === Metabolic Reconstruction === When we use the term metabolic reconstruction of a given genome we will simply mean the set of populated subsystems that contain the genome, the PEGs (and their assigned functions) that are connected to functional roles in these populated subsystems, and the specific variant code associated with the genome in each of the populated subsystems. === NMPDR pathogen genome === The NMPDR is responsible for five classes of genomes: # Campylobacter jejuni # Listeria monocytogenes # Staphylococcus aureus # Streptococcus pneumoniae and Streptococcus pyogenes # Pathogenic Vibrio === Pair of Close Homologs (PCH) === The paper [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=EBI&pubmedid=10077608 The use of gene clusters to infer functional coupling] defines a Pair of Close Homologs as follows: <blockquote> We can also define the concept of “pairs of close homologs” (PCHs) as follows: genes (X′a, Y′a) from Ga and (X′b, Y′b) from Gb form a PCH if and only if X′a and Y′a are close, X′b and Y′b are close, X′a and X′b are recognizably similar, and Y′a and Y′b are recognizably similar. Here, we will consider two genes to be recognizably similar if their gene products produce fasta3 scores lower than 1.0 × 10−5. We use a scoring scheme analogous to the one described for PCBBHs to evaluate the connections between PCHs, except that if Ga and Gb are the same genome, we assign an arbitrary “same-genome score” (“same-genome” pairs cannot occur for PCBBHs by definition, but for PCHs they are possible). Unlike PCBBHs from two very close genomes for which contiguity is completely uninformative in the vast majority of cases, PCHs allow recognition of gene clusters that play similar (but usually not identical) roles (such as two transport cassettes containing pairs of homologs) in the same or similar organisms. The arbitrary “same-genome score” should, we believe, have a value that is high enough to rank such instances as significant. </blockquote> === PEG === A Protein Encoding Gene (PEG) is equivalent to a CDS (Coding Sequence). === Populated Subsystem === please see [[#Subsystem|Subsystem]] === SEED-Viewer === A read-only version of the SEED that presents the latest data. http://seed-viewer.theseed.org '''Please note''': The data is updated automatically every 24 hours. When citing or linking to the SEED please use this version. === Subsystem === A subsystem is a set of functional roles that an annotator has decided should be thought of as related. Frequently, subsystems represent the collection of [[#Functional_role|functional roles]] that make up a metabolic pathway, a complex (e.g., the ribosome), or a class of proteins (e.g., two-component signal-transduction proteins within Staphylococcus aureus). A '''populated subsystem''' is a subsystem with an attached spreadsheet. The rows of the spreadsheet represent genomes and the columns represent the functional roles of the spreadsheet. Each cell contains the identifiers of genes from the corresponding genome the implement the specific functional role. That is, a populated subsystem specifies which genes implement instances of the subsystem in each of the genomes. The rows of a populated genome are assigned '''variant codes''' which describe which of a set of possible variants of the subsystem exist within each genome (special codes expressing a total absence of the subsystem or remaining uncertainty exist). Construction of a large set of curated populated subsystems is at the center of the NMPDR and SEED annotation efforts. === Subsystem Clearing House === Since annotators can work on any machine (including the public SEED) the way to propagate subsystems is via http://clearinghouse.theseed.org/clearinghouse_browser.cgi? === Trial-SEED === A public, read-write copy of the SEED is made available on http://theseed.uchicago.edu/FIG/index.cgi '''Please note''': The data on this server is updated in irregular intervals. Users should not assume that annotations made on this system will persist. Please publish your annotations to the [[#Subsystem_clearing_house|Subsystem Clearing house]]. === Variant Code=== please see [[#Subsystem|Subsystem]] 23fe3f06f0011c044d56d3d19f7be8d397fa15d0 1630 1629 2007-04-20T14:54:58Z FolkerMeyer 2 /* Linking to the SEED */ wikitext text/x-wiki === Annotators SEED === The master copy for all data in the SEED environment. Users can not access this password protected site. All annotations are made available via the [[#SEED-Viewer| SEED-Viewer]] and the [[#Trial-SEED|Trial-SEED]]. === Annotation === please see [[#Assigning_a_gene_function_and_annotation| Assigning a gene function and annotation]] === Assigning a gene function and annotation === Annotators assign gene functions to genes, and we call this process annotation. In most contexts, people use the term annotation to refer to assignments of function to the genes within a single organism. We certainly use the term in this sense, but we also use it to describe the process of assigning functions to corresponding genes from numerous genomes. Our basic approach to annotation is to ask our annotators to annotate the genes included in a [[#subsystem|Subsystem]] (e.g., glycolysis) across all genomes. This process of annotation of the genes within a subsystem across a set of genomes, rather than annotation of genes within a single genome, allows our annotators to focus on a constrained set of functional roles and attempt to accurately identify exactly what variant, if any, of a subsystem exists in each of the genomes. We use the term annotation to refer to assigning functions to genes (either within a single organism or to a constrained set of gene/protein families across a set of organisms). This activity certainly is closely related to the construction of subsystems and protein families (which we call FIGfams), but we will describe those activities elsewhere. === Assignment === please see [[#Assigning_a_gene_function_and_annotation| Assigning a gene function and annotation]] === Bidirectional Best Hit (BBH) === The paper [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=EBI&pubmedid=10077608 The use of gene clusters to infer functional coupling] defines a Bidirectional Best Hit or BBH as follows: <blockquote> Given two genes Xa and Xb from two genomes Ga and Gb, Xa and Xb are called a “bidirectional best hit (BBH)” if and only if recognizable similarity exists between them (in our case, we required fasta3 scores lower than 1.0 × 10−5), there is no gene Zb in Gb that is more similar than Xb is to Xa, and there is no gene Za in Ga that is more similar than Xa is to Xb. Genes (Xa, Ya) from Ga and (Xb, Yb) from Gb form a “pair of close bidirectional best hits (PCBBH)” if and only if Xa and Ya are close, Xb and Yb are close, Xa and Xb are a BBH, and Ya and Yb are a BBH. </blockquote> === Clearinghouse === please see [[#SubsystemClearinghouse|Subsystem Clearinghouse]] ===Feature=== A feature is a defined region in the DNA. A PEG is the most prevalent feature type in the SEED. Some other feature types include RNA, prophage and pathogenicity islands. The format for a feature ID is fig|genome_id.feature_abbreviation.feature_number (ie fig|83333.1.peg.100 ). === FIGfam === FIGfams are protein families generated by the Fellowship for Interpretation of Genomes (FIG). These families are based on the collection of subsystems, as well as correspondences between genes in closely related strains (we describe the construction of FIGfams in a separate SOP). The important properties of these families are as follows: # Two PEGs which both occur within a single FIGfam are believed to have the same function. # There is a decision procedure associated with the family which can be invoked to determine whether or not a gene can be “safely” assigned the function associated with the family. === Functional role === The concept of functional role is both basic and primitive in the sense that we will not pretend to offer a precise definition. It corresponds roughly to a single logical role that a gene or gene product may play in the operation of a cell. === Gene function === The function of a protein-encoding gene (PEG) is the functional role played by the product of the gene or an expression describing a set of roles played by the encoded protein. The operators used to construct expressions and the meanings associated with the operators are described in http://www.nmpdr.org/FIG/Html/SEED_functions.html Genes other than PEGs can also be assigned functions (e.g., SSU rRNA). However, in most cases the functions assigned to genes other than PEGs tend not to be problematic. === Linking to the SEED === We support linking to the SEED using a generic mechanism: Base URL: http://www.theseed.org/linkin.cgi? {| |+ Supported SEED Identifiers for external use ! Entity type !! key !! identifier !! Example |- | Genome || genome || fig<nowiki>|</nowiki>83331.1 || [[http://www.theseed.org/linkin.cgi?genome=fig|83333.1 http://www.theseed.org/linkin.cgi?genome=fig&#124;83333.1]] |- | PEG || id || fig<nowiki>|</nowiki>83331.peg.123 || [[http://www.theseed.org/linkin.cgi?id=fig|83333.1.peg.123 http://www.theseed.org/linkin.cgi?id=fig&#124;83333.1.peg.123]] |- | RNA feature || id || fig<nowiki>|</nowiki>83331.rna.1 || [[http://www.theseed.org/linkin.cgi?id=fig|83333.1.rna.1 http://www.theseed.org/linkin.cgi?id=fig&#124;83333.1.rna.1]] |- |} SEED identifiers contain the NCBI taxonomy ID, thus if the taxonomy ID changes, we need to update our internal data accordingly. To provide stable external identifiers, we keep a list of IDs that have changed and display warning message informing the user of the change and provide a link to the new version of the data requested. === Metabolic Reconstruction === When we use the term metabolic reconstruction of a given genome we will simply mean the set of populated subsystems that contain the genome, the PEGs (and their assigned functions) that are connected to functional roles in these populated subsystems, and the specific variant code associated with the genome in each of the populated subsystems. === NMPDR pathogen genome === The NMPDR is responsible for five classes of genomes: # Campylobacter jejuni # Listeria monocytogenes # Staphylococcus aureus # Streptococcus pneumoniae and Streptococcus pyogenes # Pathogenic Vibrio === Pair of Close Homologs (PCH) === The paper [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=EBI&pubmedid=10077608 The use of gene clusters to infer functional coupling] defines a Pair of Close Homologs as follows: <blockquote> We can also define the concept of “pairs of close homologs” (PCHs) as follows: genes (X′a, Y′a) from Ga and (X′b, Y′b) from Gb form a PCH if and only if X′a and Y′a are close, X′b and Y′b are close, X′a and X′b are recognizably similar, and Y′a and Y′b are recognizably similar. Here, we will consider two genes to be recognizably similar if their gene products produce fasta3 scores lower than 1.0 × 10−5. We use a scoring scheme analogous to the one described for PCBBHs to evaluate the connections between PCHs, except that if Ga and Gb are the same genome, we assign an arbitrary “same-genome score” (“same-genome” pairs cannot occur for PCBBHs by definition, but for PCHs they are possible). Unlike PCBBHs from two very close genomes for which contiguity is completely uninformative in the vast majority of cases, PCHs allow recognition of gene clusters that play similar (but usually not identical) roles (such as two transport cassettes containing pairs of homologs) in the same or similar organisms. The arbitrary “same-genome score” should, we believe, have a value that is high enough to rank such instances as significant. </blockquote> === PEG === A Protein Encoding Gene (PEG) is equivalent to a CDS (Coding Sequence). === Populated Subsystem === please see [[#Subsystem|Subsystem]] === SEED-Viewer === A read-only version of the SEED that presents the latest data. http://seed-viewer.theseed.org '''Please note''': The data is updated automatically every 24 hours. When citing or linking to the SEED please use this version. === Subsystem === A subsystem is a set of functional roles that an annotator has decided should be thought of as related. Frequently, subsystems represent the collection of [[#Functional_role|functional roles]] that make up a metabolic pathway, a complex (e.g., the ribosome), or a class of proteins (e.g., two-component signal-transduction proteins within Staphylococcus aureus). A '''populated subsystem''' is a subsystem with an attached spreadsheet. The rows of the spreadsheet represent genomes and the columns represent the functional roles of the spreadsheet. Each cell contains the identifiers of genes from the corresponding genome the implement the specific functional role. That is, a populated subsystem specifies which genes implement instances of the subsystem in each of the genomes. The rows of a populated genome are assigned '''variant codes''' which describe which of a set of possible variants of the subsystem exist within each genome (special codes expressing a total absence of the subsystem or remaining uncertainty exist). Construction of a large set of curated populated subsystems is at the center of the NMPDR and SEED annotation efforts. === Subsystem Clearing House === Since annotators can work on any machine (including the public SEED) the way to propagate subsystems is via http://clearinghouse.theseed.org/clearinghouse_browser.cgi? === Trial-SEED === A public, read-write copy of the SEED is made available on http://theseed.uchicago.edu/FIG/index.cgi '''Please note''': The data on this server is updated in irregular intervals. Users should not assume that annotations made on this system will persist. Please publish your annotations to the [[#Subsystem_clearing_house|Subsystem Clearing house]]. === Variant Code=== please see [[#Subsystem|Subsystem]] e71c53cd647f2b07fff37d2f264c4f8cc16a896a 0 1374 1628 1593 2007-04-13T14:26:04Z WilliamMihalo 3 wikitext text/x-wiki The people behind SEED are the following: * [http://www.thefig.info FIG] ** Ross Overbeek ** Veronika Vonstein ** Gordon Pusch ** Bruce Parrello ** Rob Edwards ** Andrei Osterman ** Michael Fonstein ** Svetlana Gerdes ** Olga Zagnitko ** Olga Vassieva ** Yakov Kogan ** Irina Goltsman * [http://www.mcs.anl.gov Mathematics and Computer Science Department] [http://www.anl.gov Argonne National Labs] ** Rick Stevens ** Terry Disz ** Robert Olson ** Folker Meyer * [http://www.ci.uchicago.ed Computation Institute] [http://www.uchicago.edu University of Chicago] ** Daniela Bartels ** Matt Cohoon ** Michael Kubal ** William Mihalo ** Daniel Paarmann ** Tobias Paczian ** Andreas Wilke ** Jen Zinner * [http://www.uiuc.edu University of Illinois at Urbana-Champaign] ** Gary J. Olson ** Leslie McNeil * [http://www.hope.edu Hope College] ** Matt DeJongh ** Aaron Best * [http://www.utmem.edu/ University of Memphis Tennessee] ** Rami Aziz 8865fce113a8813c04d14589071ca486cbb0bdba 0 1406 1632 2007-06-04T20:45:59Z TobiasPaczian 17 wikitext text/x-wiki The RAST Update to Version 1.2 Included the following changes: == Improved Annotation Classifications == == Improved User Interface Flow == == New Upload Formats == 7dc2ed1b20312663916946b23f5bf3f5afb3d119 1633 1632 2007-06-04T20:47:04Z TobiasPaczian 17 /* New Upload Formats */ wikitext text/x-wiki The RAST Update to Version 1.2 Included the following changes: == Improved Annotation Classifications == == Improved User Interface Flow == == New Upload Formats == In addition to being able to upload FASTA files, we also accept GenBank files. This offers you the option of either having us recall the genes, or to preserve your genecalls. c3e0b410e47f6e8ef3509a6c94112cc668a815d0 1634 1633 2007-06-04T20:47:56Z TobiasPaczian 17 /* Improved Annotation Classifications */ wikitext text/x-wiki The RAST Update to Version 1.2 Included the following changes: == Improved Annotation Classifications == Improving the annotation classification methods, we can now classify a higher percentage of genes into subsystems, while still being very conservative. == Improved User Interface Flow == == New Upload Formats == In addition to being able to upload FASTA files, we also accept GenBank files. This offers you the option of either having us recall the genes, or to preserve your genecalls. 3e0696bb7a967b93587c87a55ed5b61e101fbc4a 1635 1634 2007-06-04T20:48:53Z TobiasPaczian 17 /* Improved User Interface Flow */ wikitext text/x-wiki The RAST Update to Version 1.2 Included the following changes: == Improved Annotation Classifications == Improving the annotation classification methods, we can now classify a higher percentage of genes into subsystems, while still being very conservative. == Improved User Interface Flow == There have been various small changes to the User Interface to improve usability. == New Upload Formats == In addition to being able to upload FASTA files, we also accept GenBank files. This offers you the option of either having us recall the genes, or to preserve your genecalls. 9339b15a0c6c9a2752e282879e0530c0eb756dde 1636 1635 2007-06-05T15:04:20Z TobiasPaczian 17 wikitext text/x-wiki The RAST Update to Version 1.2 Included the following changes: == Improved Annotation Classifications == Improving the annotation classification methods, we can now classify a higher percentage of genes into subsystems, while still being very conservative. == Improved User Interface Flow == There have been various small changes to the User Interface to improve usability. == New Upload Formats == In addition to being able to upload FASTA files, we also accept GenBank files. This offers you the option of either having us recall the genes, or to preserve your genecalls. == New Features in underlying SeedViewer == === Scenarios === We now have Scenario information for every genome running through the RAST Server available in the underlying SeedViewer. The information is available on the Organism page via the menu '''This Organism''' - '''Scenarios'''. === Comparison of Metabolic Reconstruction === On the organism page in the menu '''This Organism''' the link '''Compare Metabolic Reconstruction''' is now available. It allows you to compare the presence of subsystems in two organisms. f8ae59347be04befac0f5999e6b5ca62a189e712 0 1407 1637 2007-06-07T14:17:18Z TobiasPaczian 17 wikitext text/x-wiki Currently we support two formats for uploading your files: * FASTA * GenBank a3a90f8d338ce3042cfa8f202d95c6c79a929d43 1638 1637 2007-06-07T14:24:46Z TobiasPaczian 17 wikitext text/x-wiki Currently we support two formats for uploading your files: * FASTA * GenBank For a detailed description of the FASTA format visit [http://www.example.com link title]. For a detailes description of the GenBank format visit [http://www.example.com link title]. If you believe you have uploaded a valid format, please check for these common problems: * You may not upload Word documents, StarOffice documents or the like. The meta information stored by word processors creates an invalid format. Only plain text delivers a valid format. * Your files must contain valid headers, in the case of '''FASTA''', this is the '''>''' character, followed by the unique identifier of the sequence, optionally followed by a space and a description. For '''GenBank''', the first line of the file must start with the word '''LOCUS'''. 013a89b8b8cdb976e97a43465d9067c5b50d3478 1639 1638 2007-06-07T14:51:18Z TobiasPaczian 17 wikitext text/x-wiki Currently we support two formats for uploading your files: * FASTA * GenBank For a detailed description of the FASTA format visit [http://en.wikipedia.org/wiki/Fasta_format here]. For a detailes description of the GenBank format visit [http://www.ncbi.nlm.nih.gov/Sitemap/samplerecord.html here]. If you believe you have uploaded a valid format, please check for these common problems: * You may not upload Word documents, StarOffice documents or the like. The meta information stored by word processors creates an invalid format. Only plain text delivers a valid format. * Your files must contain valid headers, in the case of '''FASTA''', this is the '''>''' character, followed by the unique identifier of the sequence, optionally followed by a space and a description. For '''GenBank''', the first line of the file must start with the word '''LOCUS'''. ff5da8e32603e65dfb91f1f85e8d06025ae579fc 8 1090 1640 1591 2007-06-11T19:59:36Z Marland 16 wikitext text/x-wiki * navigation ** Home_of_the_SEED|Home of the SEED ** Annotating_1000_genomes|Manifesto ** SEED_People| SEED People ** Contact| Contact * SEEDs ** http://seed-viewer.theseed.org/|SEED-Viewer ** http://theseed.uchicago.edu/FIG/index.cgi|Trial-SEED ** http://seed.sdsu.edu/FIG/index.cgi|Metagenomics SEED * Documentation ** RAST_Tutorial|RAST Server Tutorial ** SEED_Viewer_Tutorial|SEED Viewer Tutorial * Miscellaneous ** DownloadPage|Download Page ** Glossary|Glossary ** SOPs|SOPs ** SpecialPurposeDBs|Special Purpose DBs aa1321d47fe1e819a1b8b4c932d1b08240598089 1662 1640 2007-06-15T17:06:03Z Marland 16 wikitext text/x-wiki * navigation ** Home_of_the_SEED|Home of the SEED ** Annotating_1000_genomes|Manifesto ** SEED_People| SEED People ** Contact| Contact * SEEDs ** http://seed-viewer.theseed.org/|SEED-Viewer ** http://theseed.uchicago.edu/FIG/index.cgi|Trial-SEED ** http://seed.sdsu.edu/FIG/index.cgi|Metagenomics SEED * Documentation ** RAST_Tutorial|RAST Server Tutorial ** SEED_Viewer_Tutorial|SEED Viewer Tutorial ** Video_Tutorials|Video Tutorials * Miscellaneous ** DownloadPage|Download Page ** Glossary|Glossary ** SOPs|SOPs ** SpecialPurposeDBs|Special Purpose DBs 21873b99f8cbb363f28aa24bf89fb639312acf85 1667 1662 2007-07-12T18:31:34Z FolkerMeyer 2 Moved pointer to new metagenomics.theseed.org CNAME for MG Rast wikitext text/x-wiki * navigation ** Home_of_the_SEED|Home of the SEED ** Annotating_1000_genomes|Manifesto ** SEED_People| SEED People ** Contact| Contact * SEEDs ** http://seed-viewer.theseed.org/|SEED-Viewer ** http://theseed.uchicago.edu/FIG/index.cgi|Trial-SEED ** http://metagenomics.theseed.org/|Metagenomics SEED * Documentation ** RAST_Tutorial|RAST Server Tutorial ** SEED_Viewer_Tutorial|SEED Viewer Tutorial ** Video_Tutorials|Video Tutorials * Miscellaneous ** DownloadPage|Download Page ** Glossary|Glossary ** SOPs|SOPs ** SpecialPurposeDBs|Special Purpose DBs 39fd4b034da0ce9bf2755bb0d494ddf565985b30 6 1408 1641 2007-06-11T21:19:21Z Marland 16 Overview of the RAST server and its connections to the SEED viewer. wikitext text/x-wiki Overview of the RAST server and its connections to the SEED viewer. 4ec1d5fbded96f1646e47ce7f6fa8f8d69438903 6 1409 1642 2007-06-11T21:21:28Z Marland 16 wikitext text/x-wiki da39a3ee5e6b4b0d3255bfef95601890afd80709 6 1410 1643 2007-06-11T21:36:18Z Marland 16 wikitext text/x-wiki da39a3ee5e6b4b0d3255bfef95601890afd80709 0 1412 1645 2007-06-11T21:39:47Z Marland 16 wikitext text/x-wiki '''The RAST Server''' The RAST (Rapid Annotation using Subsystem Technology) Server provides high quality genome annotations for prokaryotes across the whole phylogenetic tree. It makes a SEED-quality annotation available as a service with a 48 hour turnaround time. The SEED environment and SEED data structures (most prominently FIGfams) are used to compute the automatic annotations; however data is not added into the SEED automatically. Once annotation is completed, genomes can be downloaded in a variety of formats or viewed online. The genome annotation provided does include a mapping of genes to subsystems and a metabolic reconstruction. Figure 1 provides an overview of the RAST Server and connections to the SEED Viewer. Getting Started: Registration is required for genome submission and viewing of results. This enables us to contact users once the computation is finished and in case the users intervention is required. [[Image:Rast_fig1.jpg]] Figure 1. Overview of the RAST Server navigation, features and capabilities. '''Jobs Overview''' Upon logging onto the server, users are directed to the “Jobs Overview” page, which as the name suggests, provides a site for job management. Jobs Overview has two main components: starting a new job and reviewing submitted/completed jobs. Start a new job. The navigation bar (Figure 2) at the top of the page provides a pull down menu for job submission, logout, and review/edit user account information. To start a new job, users should select “Upload Genome” from the navigation bar or the link near the top of the page. The user is required to provide a valid taxonomy id+, the organism’s Genus, species, and strain, as well as a nucleotide sequence file in FASTA format. Optional parameters are suggested, but not required and include genetic code, sequencing method, coverage, number of contigs and average read length. Currently the server supports genome analysis of prokaryotes with genetic codes 4 and 11. ''+Taxonomy id’s can be obtained from the NCBI taxonomy browser (http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/). Search by organism name, and the taxonomy id is returned. For example, Escherichia coli K12 has taxonomy id 83333.'' Figure 2. Jobs Overview Navigation Bar. '''Reviewing submitted/completed jobs.''' The overall status of genome analysis can be viewed from the main portion of the Jobs Overview page. This contains information regarding a user’s personal jobs and when applicable, jobs of the user’s organization. Figure 3 shows an example account where the individual does not have any personal jobs, but has access to several for their organization. The table shows each job/genome and its status and contains information including job number, name of the user who started the job, genome id (taxonomy_id. internal_id), genome name, and annotation progress. The table of jobs can be sorted on any column containing textual information. When the user has numerous genomes to select from, they can use the text boxes in the table header to search and refine the list of jobs. Clicking on the bars for a given job in the annotation progress column directs the user to the “Job Details” page where the detailed job status and access to the genome analysis can be found. Figure 3. Jobs Overview for a given account. ''' Job Details''' For a given job, the Job Details page provides the user with information regarding the status of the genome annotation progress, as well as access to the results of the analysis upon completion. Account and job management links are found in the navigation bar at the top of the Job Details page (Figure 4) includes (1) logout, (2) upload a new genome, (3) link back to the Jobs Overview, and (4) review/edit your account information. Figure 4. Job Details Navigation Bar. The Job Details page has three main functions: 1. To provide access to the results of the genome analysis via the SEED Viewer, 2. Export tool that enables the user to download the annotated genome in various formats (GTF, GenBank, GFF3, or EMBL) 3. The status of their genome analysis. Information regarding the status of each major step in the analysis process is reported which includes: o Genome upload o Genome id and Name o Job number o Name of user who created the job o Date and time of job submission o Rapid propagation (protein function annotation) o Quality check o Statistics (number of features, warnings, fatal problems) o Warnings (overlaps) o Fatal Problems (embedded genes) o Quality revision (users approval) o Similarity Computation o Bidirectional Best Hit Computation (for conserved regions and functional coupling) o Auto Assignment (to subsystems) 1e208bf4953da1e14cdc3627bfb065b7dcf070ab 1647 1645 2007-06-12T03:12:29Z Marland 16 wikitext text/x-wiki '''The RAST Server''' The RAST (Rapid Annotation using Subsystem Technology) Server provides high quality genome annotations for prokaryotes across the whole phylogenetic tree. It makes a SEED-quality annotation available as a service with a 48 hour turnaround time. The SEED environment and SEED data structures (most prominently FIGfams) are used to compute the automatic annotations; however data is not added into the SEED automatically. Once annotation is completed, genomes can be downloaded in a variety of formats or viewed online. The genome annotation provided does include a mapping of genes to subsystems and a metabolic reconstruction. Figure 1 provides an overview of the RAST Server and connections to the SEED Viewer. Getting Started: Registration is required for genome submission and viewing of results. This enables us to contact users once the computation is finished and in case the users intervention is required. [[Image:rast_fig1.jpg]] Figure 1. Overview of the RAST Server navigation, features and capabilities. '''Jobs Overview''' Upon logging onto the server, users are directed to the “Jobs Overview” page, which as the name suggests, provides a site for job management. Jobs Overview has two main components: starting a new job and reviewing submitted/completed jobs. Start a new job. The navigation bar (Figure 2) at the top of the page provides a pull down menu for job submission, logout, and review/edit user account information. To start a new job, users should select “Upload Genome” from the navigation bar or the link near the top of the page. The user is required to provide a valid taxonomy id+, the organism’s Genus, species, and strain, as well as a nucleotide sequence file in FASTA format. Optional parameters are suggested, but not required and include genetic code, sequencing method, coverage, number of contigs and average read length. Currently the server supports genome analysis of prokaryotes with genetic codes 4 and 11. ''+Taxonomy id’s can be obtained from the NCBI taxonomy browser (http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/). Search by organism name, and the taxonomy id is returned. For example, Escherichia coli K12 has taxonomy id 83333.'' Figure 2. Jobs Overview Navigation Bar. '''Reviewing submitted/completed jobs.''' The overall status of genome analysis can be viewed from the main portion of the Jobs Overview page. This contains information regarding a user’s personal jobs and when applicable, jobs of the user’s organization. Figure 3 shows an example account where the individual does not have any personal jobs, but has access to several for their organization. The table shows each job/genome and its status and contains information including job number, name of the user who started the job, genome id (taxonomy_id. internal_id), genome name, and annotation progress. The table of jobs can be sorted on any column containing textual information. When the user has numerous genomes to select from, they can use the text boxes in the table header to search and refine the list of jobs. Clicking on the bars for a given job in the annotation progress column directs the user to the “Job Details” page where the detailed job status and access to the genome analysis can be found. Figure 3. Jobs Overview for a given account. ''' Job Details''' For a given job, the Job Details page provides the user with information regarding the status of the genome annotation progress, as well as access to the results of the analysis upon completion. Account and job management links are found in the navigation bar at the top of the Job Details page (Figure 4) includes (1) logout, (2) upload a new genome, (3) link back to the Jobs Overview, and (4) review/edit your account information. Figure 4. Job Details Navigation Bar. The Job Details page has three main functions: 1. To provide access to the results of the genome analysis via the SEED Viewer, 2. Export tool that enables the user to download the annotated genome in various formats (GTF, GenBank, GFF3, or EMBL) 3. The status of their genome analysis. Information regarding the status of each major step in the analysis process is reported which includes: o Genome upload o Genome id and Name o Job number o Name of user who created the job o Date and time of job submission o Rapid propagation (protein function annotation) o Quality check o Statistics (number of features, warnings, fatal problems) o Warnings (overlaps) o Fatal Problems (embedded genes) o Quality revision (users approval) o Similarity Computation o Bidirectional Best Hit Computation (for conserved regions and functional coupling) o Auto Assignment (to subsystems) 2adfbc6cfab7ced546e150b5a6f6ac4b327cec13 1649 1647 2007-06-12T03:15:50Z Marland 16 wikitext text/x-wiki '''The RAST Server''' The RAST (Rapid Annotation using Subsystem Technology) Server provides high quality genome annotations for prokaryotes across the whole phylogenetic tree. It makes a SEED-quality annotation available as a service with a 48 hour turnaround time. The SEED environment and SEED data structures (most prominently FIGfams) are used to compute the automatic annotations; however data is not added into the SEED automatically. Once annotation is completed, genomes can be downloaded in a variety of formats or viewed online. The genome annotation provided does include a mapping of genes to subsystems and a metabolic reconstruction. Figure 1 provides an overview of the RAST Server and connections to the SEED Viewer. Getting Started: Registration is required for genome submission and viewing of results. This enables us to contact users once the computation is finished and in case the users intervention is required. [[Image:rast_fig1.jpg]] Figure 1. Overview of the RAST Server navigation, features and capabilities. '''Jobs Overview''' Upon logging onto the server, users are directed to the “Jobs Overview” page, which as the name suggests, provides a site for job management. Jobs Overview has two main components: starting a new job and reviewing submitted/completed jobs. Start a new job. The navigation bar (Figure 2) at the top of the page provides a pull down menu for job submission, logout, and review/edit user account information. To start a new job, users should select “Upload Genome” from the navigation bar or the link near the top of the page. The user is required to provide a valid taxonomy id+, the organism’s Genus, species, and strain, as well as a nucleotide sequence file in FASTA format. Optional parameters are suggested, but not required and include genetic code, sequencing method, coverage, number of contigs and average read length. Currently the server supports genome analysis of prokaryotes with genetic codes 4 and 11. ''+Taxonomy id’s can be obtained from the NCBI taxonomy browser (http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/). Search by organism name, and the taxonomy id is returned. For example, Escherichia coli K12 has taxonomy id 83333.'' [[Image:rast_fig2.jpg]] Figure 2. Jobs Overview Navigation Bar. '''Reviewing submitted/completed jobs.''' The overall status of genome analysis can be viewed from the main portion of the Jobs Overview page. This contains information regarding a user’s personal jobs and when applicable, jobs of the user’s organization. Figure 3 shows an example account where the individual does not have any personal jobs, but has access to several for their organization. The table shows each job/genome and its status and contains information including job number, name of the user who started the job, genome id (taxonomy_id. internal_id), genome name, and annotation progress. The table of jobs can be sorted on any column containing textual information. When the user has numerous genomes to select from, they can use the text boxes in the table header to search and refine the list of jobs. Clicking on the bars for a given job in the annotation progress column directs the user to the “Job Details” page where the detailed job status and access to the genome analysis can be found. Figure 3. Jobs Overview for a given account. ''' Job Details''' For a given job, the Job Details page provides the user with information regarding the status of the genome annotation progress, as well as access to the results of the analysis upon completion. Account and job management links are found in the navigation bar at the top of the Job Details page (Figure 4) includes (1) logout, (2) upload a new genome, (3) link back to the Jobs Overview, and (4) review/edit your account information. Figure 4. Job Details Navigation Bar. The Job Details page has three main functions: 1. To provide access to the results of the genome analysis via the SEED Viewer, 2. Export tool that enables the user to download the annotated genome in various formats (GTF, GenBank, GFF3, or EMBL) 3. The status of their genome analysis. Information regarding the status of each major step in the analysis process is reported which includes: o Genome upload o Genome id and Name o Job number o Name of user who created the job o Date and time of job submission o Rapid propagation (protein function annotation) o Quality check o Statistics (number of features, warnings, fatal problems) o Warnings (overlaps) o Fatal Problems (embedded genes) o Quality revision (users approval) o Similarity Computation o Bidirectional Best Hit Computation (for conserved regions and functional coupling) o Auto Assignment (to subsystems) 03771610e44a28cab42e95fe32a39df077da68ba 1650 1649 2007-06-12T03:22:02Z Marland 16 wikitext text/x-wiki '''The RAST Server''' The RAST (Rapid Annotation using Subsystem Technology) Server provides high quality genome annotations for prokaryotes across the whole phylogenetic tree. It makes a SEED-quality annotation available as a service with a 48 hour turnaround time. The SEED environment and SEED data structures (most prominently FIGfams) are used to compute the automatic annotations; however data is not added into the SEED automatically. Once annotation is completed, genomes can be downloaded in a variety of formats or viewed online. The genome annotation provided does include a mapping of genes to subsystems and a metabolic reconstruction. Figure 1 provides an overview of the RAST Server and connections to the SEED Viewer. Getting Started: Registration is required for genome submission and viewing of results. This enables us to contact users once the computation is finished and in case the users intervention is required. [[Image:rast_fig1.jpg]] Figure 1. Overview of the RAST Server navigation, features and capabilities. '''Jobs Overview''' Upon logging onto the server, users are directed to the “Jobs Overview” page, which as the name suggests, provides a site for job management. Jobs Overview has two main components: starting a new job and reviewing submitted/completed jobs. Start a new job. The navigation bar (Figure 2) at the top of the page provides a pull down menu for job submission, logout, and review/edit user account information. To start a new job, users should select “Upload Genome” from the navigation bar or the link near the top of the page. The user is required to provide a valid taxonomy id+, the organism’s Genus, species, and strain, as well as a nucleotide sequence file in FASTA format. Optional parameters are suggested, but not required and include genetic code, sequencing method, coverage, number of contigs and average read length. Currently the server supports genome analysis of prokaryotes with genetic codes 4 and 11. ''+Taxonomy id’s can be obtained from the NCBI taxonomy browser (http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/). Search by organism name, and the taxonomy id is returned. For example, Escherichia coli K12 has taxonomy id 83333.'' [[Image:rast_fig2.jpg]] Figure 2. Jobs Overview Navigation Bar. '''Reviewing submitted/completed jobs.''' The overall status of genome analysis can be viewed from the main portion of the Jobs Overview page. This contains information regarding a user’s personal jobs and when applicable, jobs of the user’s organization. Figure 3 shows an example account where the individual does not have any personal jobs, but has access to several for their organization. The table shows each job/genome and its status and contains information including job number, name of the user who started the job, genome id (taxonomy_id. internal_id), genome name, and annotation progress. The table of jobs can be sorted on any column containing textual information. When the user has numerous genomes to select from, they can use the text boxes in the table header to search and refine the list of jobs. Clicking on the bars for a given job in the annotation progress column directs the user to the “Job Details” page where the detailed job status and access to the genome analysis can be found. Figure 3. Jobs Overview for a given account. ''' Job Details''' For a given job, the Job Details page provides the user with information regarding the status of the genome annotation progress, as well as access to the results of the analysis upon completion. Account and job management links are found in the navigation bar at the top of the Job Details page (Figure 4) includes (1) logout, (2) upload a new genome, (3) link back to the Jobs Overview, and (4) review/edit your account information. Figure 4. Job Details Navigation Bar. The Job Details page has three main functions: 1. To provide access to the results of the genome analysis via the SEED Viewer, 2. Export tool that enables the user to download the annotated genome in various formats (GTF, GenBank, GFF3, or EMBL) 3. The status of their genome analysis. Information regarding the status of each major step in the analysis process is reported which includes: * Genome upload ** Genome id and Name ** Job number ** Name of user who created the job ** Date and time of job submission * Rapid propagation (protein function annotation) * Quality check ** Statistics (number of features, warnings, fatal problems) ** Warnings (overlaps) ** Fatal Problems (embedded genes) * Quality revision (users approval) * Similarity Computation * Bidirectional Best Hit Computation (for conserved regions and functional coupling) * Auto Assignment (to subsystems) bae31a2f0c374cdfc5e918a1afe9426ec89e3397 1651 1650 2007-06-12T03:22:59Z Marland 16 wikitext text/x-wiki '''The RAST Server''' The RAST (Rapid Annotation using Subsystem Technology) Server provides high quality genome annotations for prokaryotes across the whole phylogenetic tree. It makes a SEED-quality annotation available as a service with a 48 hour turnaround time. The SEED environment and SEED data structures (most prominently FIGfams) are used to compute the automatic annotations; however data is not added into the SEED automatically. Once annotation is completed, genomes can be downloaded in a variety of formats or viewed online. The genome annotation provided does include a mapping of genes to subsystems and a metabolic reconstruction. Figure 1 provides an overview of the RAST Server and connections to the SEED Viewer. Getting Started: Registration is required for genome submission and viewing of results. This enables us to contact users once the computation is finished and in case the users intervention is required. [[Image:rast_fig1.jpg]] Figure 1. Overview of the RAST Server navigation, features and capabilities. '''Jobs Overview''' Upon logging onto the server, users are directed to the “Jobs Overview” page, which as the name suggests, provides a site for job management. Jobs Overview has two main components: starting a new job and reviewing submitted/completed jobs. Start a new job. The navigation bar (Figure 2) at the top of the page provides a pull down menu for job submission, logout, and review/edit user account information. To start a new job, users should select “Upload Genome” from the navigation bar or the link near the top of the page. The user is required to provide a valid taxonomy id+, the organism’s Genus, species, and strain, as well as a nucleotide sequence file in FASTA format. Optional parameters are suggested, but not required and include genetic code, sequencing method, coverage, number of contigs and average read length. Currently the server supports genome analysis of prokaryotes with genetic codes 4 and 11. ''+Taxonomy id’s can be obtained from the NCBI taxonomy browser (http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/). Search by organism name, and the taxonomy id is returned. For example, Escherichia coli K12 has taxonomy id 83333.'' [[Image:rast_fig2.jpg]] Figure 2. Jobs Overview Navigation Bar. '''Reviewing submitted/completed jobs.''' The overall status of genome analysis can be viewed from the main portion of the Jobs Overview page. This contains information regarding a user’s personal jobs and when applicable, jobs of the user’s organization. Figure 3 shows an example account where the individual does not have any personal jobs, but has access to several for their organization. The table shows each job/genome and its status and contains information including job number, name of the user who started the job, genome id (taxonomy_id. internal_id), genome name, and annotation progress. The table of jobs can be sorted on any column containing textual information. When the user has numerous genomes to select from, they can use the text boxes in the table header to search and refine the list of jobs. Clicking on the bars for a given job in the annotation progress column directs the user to the “Job Details” page where the detailed job status and access to the genome analysis can be found. [[Image:rast_fig3.jpg]] Figure 3. Jobs Overview for a given account. ''' Job Details''' For a given job, the Job Details page provides the user with information regarding the status of the genome annotation progress, as well as access to the results of the analysis upon completion. Account and job management links are found in the navigation bar at the top of the Job Details page (Figure 4) includes (1) logout, (2) upload a new genome, (3) link back to the Jobs Overview, and (4) review/edit your account information. [[Image:rast_fig4.jpg]] Figure 4. Job Details Navigation Bar. The Job Details page has three main functions: 1. To provide access to the results of the genome analysis via the SEED Viewer, 2. Export tool that enables the user to download the annotated genome in various formats (GTF, GenBank, GFF3, or EMBL) 3. The status of their genome analysis. Information regarding the status of each major step in the analysis process is reported which includes: * Genome upload ** Genome id and Name ** Job number ** Name of user who created the job ** Date and time of job submission * Rapid propagation (protein function annotation) * Quality check ** Statistics (number of features, warnings, fatal problems) ** Warnings (overlaps) ** Fatal Problems (embedded genes) * Quality revision (users approval) * Similarity Computation * Bidirectional Best Hit Computation (for conserved regions and functional coupling) * Auto Assignment (to subsystems) 048279fc4020c4a9be3f492e1ae2e85f9ae05ff4 1654 1651 2007-06-12T03:24:42Z Marland 16 wikitext text/x-wiki '''The RAST Server''' The RAST (Rapid Annotation using Subsystem Technology) Server provides high quality genome annotations for prokaryotes across the whole phylogenetic tree. It makes a SEED-quality annotation available as a service with a 48 hour turnaround time. The SEED environment and SEED data structures (most prominently FIGfams) are used to compute the automatic annotations; however data is not added into the SEED automatically. Once annotation is completed, genomes can be downloaded in a variety of formats or viewed online. The genome annotation provided does include a mapping of genes to subsystems and a metabolic reconstruction. Figure 1 provides an overview of the RAST Server and connections to the SEED Viewer. Getting Started: Registration is required for genome submission and viewing of results. This enables us to contact users once the computation is finished and in case the users intervention is required. [[Image:rast_fig1.jpg]] Figure 1. Overview of the RAST Server navigation, features and capabilities. '''Jobs Overview''' Upon logging onto the server, users are directed to the “Jobs Overview” page, which as the name suggests, provides a site for job management. Jobs Overview has two main components: starting a new job and reviewing submitted/completed jobs. Start a new job. The navigation bar (Figure 2) at the top of the page provides a pull down menu for job submission, logout, and review/edit user account information. To start a new job, users should select “Upload Genome” from the navigation bar or the link near the top of the page. The user is required to provide a valid taxonomy id+, the organism’s Genus, species, and strain, as well as a nucleotide sequence file in FASTA format. Optional parameters are suggested, but not required and include genetic code, sequencing method, coverage, number of contigs and average read length. Currently the server supports genome analysis of prokaryotes with genetic codes 4 and 11. ''+Taxonomy id’s can be obtained from the NCBI taxonomy browser (http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/). Search by organism name, and the taxonomy id is returned. For example, Escherichia coli K12 has taxonomy id 83333.'' [[Image:rast_fig2.jpg]] Figure 2. Jobs Overview Navigation Bar. '''Reviewing submitted/completed jobs.''' The overall status of genome analysis can be viewed from the main portion of the Jobs Overview page. This contains information regarding a user’s personal jobs and when applicable, jobs of the user’s organization. Figure 3 shows an example account where the individual does not have any personal jobs, but has access to several for their organization. The table shows each job/genome and its status and contains information including job number, name of the user who started the job, genome id (taxonomy_id. internal_id), genome name, and annotation progress. The table of jobs can be sorted on any column containing textual information. When the user has numerous genomes to select from, they can use the text boxes in the table header to search and refine the list of jobs. Clicking on the bars for a given job in the annotation progress column directs the user to the “Job Details” page where the detailed job status and access to the genome analysis can be found. [[Image:rast_fig3.jpg]] Figure 3. Jobs Overview for a given account. ''' Job Details''' For a given job, the Job Details page provides the user with information regarding the status of the genome annotation progress, as well as access to the results of the analysis upon completion. Account and job management links are found in the navigation bar at the top of the Job Details page (Figure 4) includes (1) logout, (2) upload a new genome, (3) link back to the Jobs Overview, and (4) review/edit your account information. [[Image:rast_fig4.jpg]] Figure 4. Job Details Navigation Bar. The Job Details page has three main functions: 1. To provide access to the results of the genome analysis via the SEED Viewer, 2. Export tool that enables the user to download the annotated genome in various formats (GTF, GenBank, GFF3, or EMBL) 3. The status of their genome analysis. Information regarding the status of each major step in the analysis process is reported which includes: * Genome upload ** Genome id and Name ** Job number ** Name of user who created the job ** Date and time of job submission * Rapid propagation (protein function annotation) * Quality check ** Statistics (number of features, warnings, fatal problems) ** Warnings (overlaps) ** Fatal Problems (embedded genes) * Quality revision (users approval) * Similarity Computation * Bidirectional Best Hit Computation (for conserved regions and functional coupling) * Auto Assignment (to subsystems) 8dfd42e2b84ea5f1c944b840c0469e3a88701b33 6 1414 1648 2007-06-12T03:14:48Z Marland 16 wikitext text/x-wiki da39a3ee5e6b4b0d3255bfef95601890afd80709 6 1415 1652 2007-06-12T03:23:14Z Marland 16 wikitext text/x-wiki da39a3ee5e6b4b0d3255bfef95601890afd80709 6 1416 1653 2007-06-12T03:23:38Z Marland 16 wikitext text/x-wiki da39a3ee5e6b4b0d3255bfef95601890afd80709 6 1417 1655 2007-06-12T03:25:13Z Marland 16 wikitext text/x-wiki da39a3ee5e6b4b0d3255bfef95601890afd80709 0 1418 1656 2007-06-12T03:29:16Z Marland 16 wikitext text/x-wiki '''The SEED Viewer''' Selecting “Browse annotated genome in SEED Viewer” from the “Job Details” page of the RAST server will direct the user to the Organism Page in the SEED Viewer. '''Organism Page in SEED Viewer''' In the navigation bar at the top of the page adjacent to the homepage symbol is a pull down menu labeled 'This Organism' with the following 4 display options for this page: Figure 5. SEED Viewer navigation bar with links to the genome browser, genome features, reactions, and genome comparison tool. 1. Overview and Subsystems * The top of page provides summary statistics for this genome including the numbers of subsystems, coding sequences, RNAs and other background information. * A breakdown of the number of protein encoding genes with hypothetical and non-hypothetical function assignments is provided in box in the top right corner of the page. * Adjacent to the Taxonomy ID is the Wikipedia Globe that is linked to the Wikipedia entry for this organism. * On the bottom left of the page a bar graph depicts the percentages of protein encoding genes for this genome that are present in at least one subsystem. * Next to the bar graph a pie chart and accompanying expandable hierarchical tree, color coded to match the pie chart, organizes the subsystems present in this genome by cellular process. At every level in the tree the number of protein encoding genes in each category is listed in parentheses. At the leaves of the tree are links to a Subsytem page in the SEED Viewer. 2. Browse Genome * This display allows you to walk the chromosome of the selected genome. * If the genome is not completely assembled, the first contig will be selected. * The window size in terms of number of base pairs can be selected using the 'Window Size' pulldown menu or the 'zoom in' or 'zoom out' buttons. * The < and > buttons will move the window down or up the chromosome half the window size. * The << and >> buttons will move the window down or up the chromosome a full window size. * Under 'Options' you can select which features and the number of strands or reading frames displayed. By default the genome browser offers a two strand view of the currently selected organism. * After selecting your options, click the 'Refresh' button to update the page. * On the middle line of the chromosome display you will see features not associated with a reading frame, such as RNAs, pathogenicity islands or prophages. * Hover over a feature in the chromosome display for a detailed description. * Clicking an item will take you to the Annotation page in the SEED Viewer for this feature. 3. View Features * Selecting this display provides a table containing feature ID, functional assignment, starting and stopping location in terms of base pairs relative to the beginning of the contig, feature type and a list of aliases. * The total number of features for this genome is displayed above the table. * Use the 'next>>' and 'last>>' links to quickly scroll through sets of 10 features. * Filter features across the entire genome by using the text entry boxes in the 'Functional Assignment', 'Type' or 'Aliases' column header and then hitting enter. * Sort or reverse sort the tables using the triangle in the columns headers. * Export all or a subset of the features, after filtering, of a genome to a spreadsheet file using the 'Export Table' button. 4. View Reactions * For each genome, the genes that are part of known subsystems are compiled as an expandable hierarchical tree. This organizes the subsystems present in this genome by cellular process. * The next level in the tree shows all the reactions for a given cellular process with links to KEGG for complete reaction details. * At the leaves of the tree are the fig ids for all proteins annotated as those which catalyze the reaction. These proteins are linked to an Annotation Overview in the SEED Viewer. 5. Compare Genome This tool allows the user to identify protein functions that are the same or different for a set of organisms. The results are presented in tabular form with information regarding function, EC and subsystem involvement displayed. Each protein is linked to the Annotation Overview in the SEED Viewer. 6. Annotation Overview * This page offers access to the data relating to a feature. By default the Overview version of the page is initially displayed providing the feature's function assignment, source organism, the role it performs in a subsystem, and a graphic displaying its genomic context. If this feature's function is associated with one or more functional roles, each functional role's name will be displayed and linked to a SEED Viewer Functional Role page. A part of a feature's function that is not also a functional role is NOT linked. * If this feature is included in a subsystem, detailed information about this feature's role or roles in one or more subsystems is provided in a shaded box at the top of the page on the right. The functional role names and subsystem names are linked to the SEED Viewer Functional Role page and the SEED Viewer Subsystem page. * In the graphic each line represents a different genome. The genome of the feature that is the subject of this page is on the first line with the subject feature in red and centered in a 16kb window. Features on the same line that have a gray shadow are functionally coupled to the subject feature. Features in different genome that share the same color or number are similar. Clicking 'Diverse Genomes' will change the genomes in the graphic to a set that is more phylogentically distant to the subject feature's genome. * If there are no close genomes only a single line for the subject feature's genome will be present. * If no data for diverse genomes has been computed a message saying so will be be displayed. Sequence Data - From the green bar at the top of page, selecting the 'This Protein' menu will give the user the choice of viewing the this feature's DNA sequence, DNA with flanking sequence or amino acid sequence. Tools - From the green bar at the top of the page, selecting the 'Tools' menu will give the user the choice of the following tools to analyze this feature: * TMpred (transmembrane helix prediction) * TMHMM (transmembrane helix prediction) * Gram negative PSORT (subcellular localization prediction) * Gram negative SignalP (signal sequence prediction) * Gram positive PSORT (subcellular localization prediction) * Gram positive SignalP (signal sequence prediction) * LipoP (lipoprotein prediction) * InterProScan (protein domain identification) * Radar (detection of protein sequence repeats) * PPSearch (protein motif identification) * Gram negative CELLO (subcellular localization prediction) * Gram positive CELLO (subcellular localization prediction) * ProDom (protein domain identification) Literature - This menu list links to sources of literature discussing this specific feature. Currently PubMed is the only source. 7. Functional Role * This page displays statistics on the number of protein encoding genes within the SEED database that currently are associated with this functional role and within how many different organisms these genes are present. * In addition, this page lists the subsystem(s) for a functional role and if present, EC number, associated GO terms, and KEGG reaction. * A table lists all occurrences of the functional role in the SEED database. Figure 6. Flowchart for navigating the RAST Server and SEED Viewer. Arrows indicate how users can access the various pages within the system. ea23ffc8fc1b982a629e9286bd56f24ba530a558 1657 1656 2007-06-12T03:32:31Z Marland 16 wikitext text/x-wiki '''The SEED Viewer''' Selecting “Browse annotated genome in SEED Viewer” from the “Job Details” page of the RAST server will direct the user to the Organism Page in the SEED Viewer. '''Organism Page in SEED Viewer''' In the navigation bar at the top of the page adjacent to the homepage symbol is a pull down menu labeled 'This Organism' with the following 4 display options for this page: [[Image:seed_fig1.jpg]] Figure 1. SEED Viewer navigation bar with links to the genome browser, genome features, reactions, and genome comparison tool. 1. Overview and Subsystems * The top of page provides summary statistics for this genome including the numbers of subsystems, coding sequences, RNAs and other background information. * A breakdown of the number of protein encoding genes with hypothetical and non-hypothetical function assignments is provided in box in the top right corner of the page. * Adjacent to the Taxonomy ID is the Wikipedia Globe that is linked to the Wikipedia entry for this organism. * On the bottom left of the page a bar graph depicts the percentages of protein encoding genes for this genome that are present in at least one subsystem. * Next to the bar graph a pie chart and accompanying expandable hierarchical tree, color coded to match the pie chart, organizes the subsystems present in this genome by cellular process. At every level in the tree the number of protein encoding genes in each category is listed in parentheses. At the leaves of the tree are links to a Subsytem page in the SEED Viewer. 2. Browse Genome * This display allows you to walk the chromosome of the selected genome. * If the genome is not completely assembled, the first contig will be selected. * The window size in terms of number of base pairs can be selected using the 'Window Size' pulldown menu or the 'zoom in' or 'zoom out' buttons. * The < and > buttons will move the window down or up the chromosome half the window size. * The << and >> buttons will move the window down or up the chromosome a full window size. * Under 'Options' you can select which features and the number of strands or reading frames displayed. By default the genome browser offers a two strand view of the currently selected organism. * After selecting your options, click the 'Refresh' button to update the page. * On the middle line of the chromosome display you will see features not associated with a reading frame, such as RNAs, pathogenicity islands or prophages. * Hover over a feature in the chromosome display for a detailed description. * Clicking an item will take you to the Annotation page in the SEED Viewer for this feature. 3. View Features * Selecting this display provides a table containing feature ID, functional assignment, starting and stopping location in terms of base pairs relative to the beginning of the contig, feature type and a list of aliases. * The total number of features for this genome is displayed above the table. * Use the 'next>>' and 'last>>' links to quickly scroll through sets of 10 features. * Filter features across the entire genome by using the text entry boxes in the 'Functional Assignment', 'Type' or 'Aliases' column header and then hitting enter. * Sort or reverse sort the tables using the triangle in the columns headers. * Export all or a subset of the features, after filtering, of a genome to a spreadsheet file using the 'Export Table' button. 4. View Reactions * For each genome, the genes that are part of known subsystems are compiled as an expandable hierarchical tree. This organizes the subsystems present in this genome by cellular process. * The next level in the tree shows all the reactions for a given cellular process with links to KEGG for complete reaction details. * At the leaves of the tree are the fig ids for all proteins annotated as those which catalyze the reaction. These proteins are linked to an Annotation Overview in the SEED Viewer. 5. Compare Genome This tool allows the user to identify protein functions that are the same or different for a set of organisms. The results are presented in tabular form with information regarding function, EC and subsystem involvement displayed. Each protein is linked to the Annotation Overview in the SEED Viewer. 6. Annotation Overview * This page offers access to the data relating to a feature. By default the Overview version of the page is initially displayed providing the feature's function assignment, source organism, the role it performs in a subsystem, and a graphic displaying its genomic context. If this feature's function is associated with one or more functional roles, each functional role's name will be displayed and linked to a SEED Viewer Functional Role page. A part of a feature's function that is not also a functional role is NOT linked. * If this feature is included in a subsystem, detailed information about this feature's role or roles in one or more subsystems is provided in a shaded box at the top of the page on the right. The functional role names and subsystem names are linked to the SEED Viewer Functional Role page and the SEED Viewer Subsystem page. * In the graphic each line represents a different genome. The genome of the feature that is the subject of this page is on the first line with the subject feature in red and centered in a 16kb window. Features on the same line that have a gray shadow are functionally coupled to the subject feature. Features in different genome that share the same color or number are similar. Clicking 'Diverse Genomes' will change the genomes in the graphic to a set that is more phylogentically distant to the subject feature's genome. * If there are no close genomes only a single line for the subject feature's genome will be present. * If no data for diverse genomes has been computed a message saying so will be be displayed. ''Sequence Data'' - From the green bar at the top of page, selecting the 'This Protein' menu will give the user the choice of viewing the this feature's DNA sequence, DNA with flanking sequence or amino acid sequence. ''Tools'' - From the green bar at the top of the page, selecting the 'Tools' menu will give the user the choice of the following tools to analyze this feature: * TMpred (transmembrane helix prediction) * TMHMM (transmembrane helix prediction) * Gram negative PSORT (subcellular localization prediction) * Gram negative SignalP (signal sequence prediction) * Gram positive PSORT (subcellular localization prediction) * Gram positive SignalP (signal sequence prediction) * LipoP (lipoprotein prediction) * InterProScan (protein domain identification) * Radar (detection of protein sequence repeats) * PPSearch (protein motif identification) * Gram negative CELLO (subcellular localization prediction) * Gram positive CELLO (subcellular localization prediction) * ProDom (protein domain identification) ''Literature'' - This menu list links to sources of literature discussing this specific feature. Currently PubMed is the only source. 7. Functional Role * This page displays statistics on the number of protein encoding genes within the SEED database that currently are associated with this functional role and within how many different organisms these genes are present. * In addition, this page lists the subsystem(s) for a functional role and if present, EC number, associated GO terms, and KEGG reaction. * A table lists all occurrences of the functional role in the SEED database. [[Image:seed_fig2.jpg]] Figure 2. Flowchart for navigating the RAST Server and SEED Viewer. Arrows indicate how users can access the various pages within the system. f9419f5a18a9c9bcb31deb8c9a65c78d1e89822c 1658 1657 2007-06-12T03:32:40Z Marland 16 wikitext text/x-wiki '''The SEED Viewer''' Selecting “Browse annotated genome in SEED Viewer” from the “Job Details” page of the RAST server will direct the user to the Organism Page in the SEED Viewer. '''Organism Page in SEED Viewer''' In the navigation bar at the top of the page adjacent to the homepage symbol is a pull down menu labeled 'This Organism' with the following 4 display options for this page: [[Image:seed_fig1.jpg]] Figure 1. SEED Viewer navigation bar with links to the genome browser, genome features, reactions, and genome comparison tool. 1. Overview and Subsystems * The top of page provides summary statistics for this genome including the numbers of subsystems, coding sequences, RNAs and other background information. * A breakdown of the number of protein encoding genes with hypothetical and non-hypothetical function assignments is provided in box in the top right corner of the page. * Adjacent to the Taxonomy ID is the Wikipedia Globe that is linked to the Wikipedia entry for this organism. * On the bottom left of the page a bar graph depicts the percentages of protein encoding genes for this genome that are present in at least one subsystem. * Next to the bar graph a pie chart and accompanying expandable hierarchical tree, color coded to match the pie chart, organizes the subsystems present in this genome by cellular process. At every level in the tree the number of protein encoding genes in each category is listed in parentheses. At the leaves of the tree are links to a Subsytem page in the SEED Viewer. 2. Browse Genome * This display allows you to walk the chromosome of the selected genome. * If the genome is not completely assembled, the first contig will be selected. * The window size in terms of number of base pairs can be selected using the 'Window Size' pulldown menu or the 'zoom in' or 'zoom out' buttons. * The < and > buttons will move the window down or up the chromosome half the window size. * The << and >> buttons will move the window down or up the chromosome a full window size. * Under 'Options' you can select which features and the number of strands or reading frames displayed. By default the genome browser offers a two strand view of the currently selected organism. * After selecting your options, click the 'Refresh' button to update the page. * On the middle line of the chromosome display you will see features not associated with a reading frame, such as RNAs, pathogenicity islands or prophages. * Hover over a feature in the chromosome display for a detailed description. * Clicking an item will take you to the Annotation page in the SEED Viewer for this feature. 3. View Features * Selecting this display provides a table containing feature ID, functional assignment, starting and stopping location in terms of base pairs relative to the beginning of the contig, feature type and a list of aliases. * The total number of features for this genome is displayed above the table. * Use the 'next>>' and 'last>>' links to quickly scroll through sets of 10 features. * Filter features across the entire genome by using the text entry boxes in the 'Functional Assignment', 'Type' or 'Aliases' column header and then hitting enter. * Sort or reverse sort the tables using the triangle in the columns headers. * Export all or a subset of the features, after filtering, of a genome to a spreadsheet file using the 'Export Table' button. 4. View Reactions * For each genome, the genes that are part of known subsystems are compiled as an expandable hierarchical tree. This organizes the subsystems present in this genome by cellular process. * The next level in the tree shows all the reactions for a given cellular process with links to KEGG for complete reaction details. * At the leaves of the tree are the fig ids for all proteins annotated as those which catalyze the reaction. These proteins are linked to an Annotation Overview in the SEED Viewer. 5. Compare Genome This tool allows the user to identify protein functions that are the same or different for a set of organisms. The results are presented in tabular form with information regarding function, EC and subsystem involvement displayed. Each protein is linked to the Annotation Overview in the SEED Viewer. 6. Annotation Overview * This page offers access to the data relating to a feature. By default the Overview version of the page is initially displayed providing the feature's function assignment, source organism, the role it performs in a subsystem, and a graphic displaying its genomic context. If this feature's function is associated with one or more functional roles, each functional role's name will be displayed and linked to a SEED Viewer Functional Role page. A part of a feature's function that is not also a functional role is NOT linked. * If this feature is included in a subsystem, detailed information about this feature's role or roles in one or more subsystems is provided in a shaded box at the top of the page on the right. The functional role names and subsystem names are linked to the SEED Viewer Functional Role page and the SEED Viewer Subsystem page. * In the graphic each line represents a different genome. The genome of the feature that is the subject of this page is on the first line with the subject feature in red and centered in a 16kb window. Features on the same line that have a gray shadow are functionally coupled to the subject feature. Features in different genome that share the same color or number are similar. Clicking 'Diverse Genomes' will change the genomes in the graphic to a set that is more phylogentically distant to the subject feature's genome. * If there are no close genomes only a single line for the subject feature's genome will be present. * If no data for diverse genomes has been computed a message saying so will be be displayed. ''Sequence Data'' - From the green bar at the top of page, selecting the 'This Protein' menu will give the user the choice of viewing the this feature's DNA sequence, DNA with flanking sequence or amino acid sequence. ''Tools'' - From the green bar at the top of the page, selecting the 'Tools' menu will give the user the choice of the following tools to analyze this feature: * TMpred (transmembrane helix prediction) * TMHMM (transmembrane helix prediction) * Gram negative PSORT (subcellular localization prediction) * Gram negative SignalP (signal sequence prediction) * Gram positive PSORT (subcellular localization prediction) * Gram positive SignalP (signal sequence prediction) * LipoP (lipoprotein prediction) * InterProScan (protein domain identification) * Radar (detection of protein sequence repeats) * PPSearch (protein motif identification) * Gram negative CELLO (subcellular localization prediction) * Gram positive CELLO (subcellular localization prediction) * ProDom (protein domain identification) ''Literature'' - This menu list links to sources of literature discussing this specific feature. Currently PubMed is the only source. 7. Functional Role * This page displays statistics on the number of protein encoding genes within the SEED database that currently are associated with this functional role and within how many different organisms these genes are present. * In addition, this page lists the subsystem(s) for a functional role and if present, EC number, associated GO terms, and KEGG reaction. * A table lists all occurrences of the functional role in the SEED database. [[Image:seed_fig2.jpg]] Figure 2. Flowchart for navigating the RAST Server and SEED Viewer. Arrows indicate how users can access the various pages within the system. 22dcef15dd01c3ab2e5aa3ada75a8bb88fa3b871 1661 1658 2007-06-12T03:33:42Z Marland 16 wikitext text/x-wiki '''The SEED Viewer''' Selecting “Browse annotated genome in SEED Viewer” from the “Job Details” page of the RAST server will direct the user to the Organism Page in the SEED Viewer. '''Organism Page in SEED Viewer''' In the navigation bar at the top of the page adjacent to the homepage symbol is a pull down menu labeled 'This Organism' with the following 4 display options for this page: [[Image:Seed_fig1.jpg]] Figure 1. SEED Viewer navigation bar with links to the genome browser, genome features, reactions, and genome comparison tool. 1. Overview and Subsystems * The top of page provides summary statistics for this genome including the numbers of subsystems, coding sequences, RNAs and other background information. * A breakdown of the number of protein encoding genes with hypothetical and non-hypothetical function assignments is provided in box in the top right corner of the page. * Adjacent to the Taxonomy ID is the Wikipedia Globe that is linked to the Wikipedia entry for this organism. * On the bottom left of the page a bar graph depicts the percentages of protein encoding genes for this genome that are present in at least one subsystem. * Next to the bar graph a pie chart and accompanying expandable hierarchical tree, color coded to match the pie chart, organizes the subsystems present in this genome by cellular process. At every level in the tree the number of protein encoding genes in each category is listed in parentheses. At the leaves of the tree are links to a Subsytem page in the SEED Viewer. 2. Browse Genome * This display allows you to walk the chromosome of the selected genome. * If the genome is not completely assembled, the first contig will be selected. * The window size in terms of number of base pairs can be selected using the 'Window Size' pulldown menu or the 'zoom in' or 'zoom out' buttons. * The < and > buttons will move the window down or up the chromosome half the window size. * The << and >> buttons will move the window down or up the chromosome a full window size. * Under 'Options' you can select which features and the number of strands or reading frames displayed. By default the genome browser offers a two strand view of the currently selected organism. * After selecting your options, click the 'Refresh' button to update the page. * On the middle line of the chromosome display you will see features not associated with a reading frame, such as RNAs, pathogenicity islands or prophages. * Hover over a feature in the chromosome display for a detailed description. * Clicking an item will take you to the Annotation page in the SEED Viewer for this feature. 3. View Features * Selecting this display provides a table containing feature ID, functional assignment, starting and stopping location in terms of base pairs relative to the beginning of the contig, feature type and a list of aliases. * The total number of features for this genome is displayed above the table. * Use the 'next>>' and 'last>>' links to quickly scroll through sets of 10 features. * Filter features across the entire genome by using the text entry boxes in the 'Functional Assignment', 'Type' or 'Aliases' column header and then hitting enter. * Sort or reverse sort the tables using the triangle in the columns headers. * Export all or a subset of the features, after filtering, of a genome to a spreadsheet file using the 'Export Table' button. 4. View Reactions * For each genome, the genes that are part of known subsystems are compiled as an expandable hierarchical tree. This organizes the subsystems present in this genome by cellular process. * The next level in the tree shows all the reactions for a given cellular process with links to KEGG for complete reaction details. * At the leaves of the tree are the fig ids for all proteins annotated as those which catalyze the reaction. These proteins are linked to an Annotation Overview in the SEED Viewer. 5. Compare Genome This tool allows the user to identify protein functions that are the same or different for a set of organisms. The results are presented in tabular form with information regarding function, EC and subsystem involvement displayed. Each protein is linked to the Annotation Overview in the SEED Viewer. 6. Annotation Overview * This page offers access to the data relating to a feature. By default the Overview version of the page is initially displayed providing the feature's function assignment, source organism, the role it performs in a subsystem, and a graphic displaying its genomic context. If this feature's function is associated with one or more functional roles, each functional role's name will be displayed and linked to a SEED Viewer Functional Role page. A part of a feature's function that is not also a functional role is NOT linked. * If this feature is included in a subsystem, detailed information about this feature's role or roles in one or more subsystems is provided in a shaded box at the top of the page on the right. The functional role names and subsystem names are linked to the SEED Viewer Functional Role page and the SEED Viewer Subsystem page. * In the graphic each line represents a different genome. The genome of the feature that is the subject of this page is on the first line with the subject feature in red and centered in a 16kb window. Features on the same line that have a gray shadow are functionally coupled to the subject feature. Features in different genome that share the same color or number are similar. Clicking 'Diverse Genomes' will change the genomes in the graphic to a set that is more phylogentically distant to the subject feature's genome. * If there are no close genomes only a single line for the subject feature's genome will be present. * If no data for diverse genomes has been computed a message saying so will be be displayed. ''Sequence Data'' - From the green bar at the top of page, selecting the 'This Protein' menu will give the user the choice of viewing the this feature's DNA sequence, DNA with flanking sequence or amino acid sequence. ''Tools'' - From the green bar at the top of the page, selecting the 'Tools' menu will give the user the choice of the following tools to analyze this feature: * TMpred (transmembrane helix prediction) * TMHMM (transmembrane helix prediction) * Gram negative PSORT (subcellular localization prediction) * Gram negative SignalP (signal sequence prediction) * Gram positive PSORT (subcellular localization prediction) * Gram positive SignalP (signal sequence prediction) * LipoP (lipoprotein prediction) * InterProScan (protein domain identification) * Radar (detection of protein sequence repeats) * PPSearch (protein motif identification) * Gram negative CELLO (subcellular localization prediction) * Gram positive CELLO (subcellular localization prediction) * ProDom (protein domain identification) ''Literature'' - This menu list links to sources of literature discussing this specific feature. Currently PubMed is the only source. 7. Functional Role * This page displays statistics on the number of protein encoding genes within the SEED database that currently are associated with this functional role and within how many different organisms these genes are present. * In addition, this page lists the subsystem(s) for a functional role and if present, EC number, associated GO terms, and KEGG reaction. * A table lists all occurrences of the functional role in the SEED database. [[Image:Seed_fig2.jpg]] Figure 2. Flowchart for navigating the RAST Server and SEED Viewer. Arrows indicate how users can access the various pages within the system. 638d48d935bfa4555bb6c72e7292c0b638d88673 6 1419 1659 2007-06-12T03:32:57Z Marland 16 wikitext text/x-wiki da39a3ee5e6b4b0d3255bfef95601890afd80709 6 1420 1660 2007-06-12T03:33:16Z Marland 16 wikitext text/x-wiki da39a3ee5e6b4b0d3255bfef95601890afd80709 0 1421 1663 2007-06-15T17:13:43Z Marland 16 wikitext text/x-wiki '''RAST Sever Video Tutorials''' * RAST User Registration :: [[Media:Example1.ogg]] * RAST Genome Submission :: [[Media:Example2.ogg]] * RAST Access and Export of Genome Analysis :: [[Media:Example3.ogg]] 6b398cf983e5d67e9fff26c78fb37cc40f0bbe8a 1665 1663 2007-06-15T20:03:55Z Marland 16 wikitext text/x-wiki '''RAST Sever Video Tutorials''' * RAST User Registration ftp://ftp.theseed.org/misc/Workshop_AVIs/rast_registration.avi * RAST Genome Submission ftp://ftp.theseed.org/misc/Workshop_AVIs/rast_upload.avi * RAST Access and Export of Genome Analysis ftp://ftp.theseed.org/misc/Workshop_AVIs/rast_export.avi 4d6d8e96c90d137711014523f4606c846a14275a 0 1422 1668 2007-07-23T20:43:05Z BruceParrello 19 Overview of the NMPDR Search Facility wikitext text/x-wiki The NMPDR search facility provides many different ways to look for genes, genomes, or sequences in the NMPDR database. The following searches are currently supported. {| | '''[[OpSearch]]''' || Display genes of a single genome organized into operons. |- | '''[[WordSearch]]''' || Display genes that match certain keywords. |- | '''[[FidSearch]]''' || Display genes from one or more genomes filtered by subsystem or keywords. |- | '''[[SigGenes]]''' || Display genes that are common to a set of genomes, or that differentiate between two sets of genomes. |- | '''[[ToolSearch]]''' || Search for genes or DNA using BLAST or pattern-matching. |- | '''[[SubSearch]]''' || Search for genes in a given subsystem or subsystem class. |- | '''[[DrugSearch]]''' || Show ''in silico'' docking results for select PDBs. |} All NMPDR searches allow you to download results in tab-delimited and XML formats. NMPDR searches that return a list of genes allow you to download the genes in FASTA format. ff2bff44b6ee3361cc9f0dac833ed3dc3e6c7740 1669 1668 2007-07-23T20:48:25Z BruceParrello 19 An overview of the NMPDR search facility wikitext text/x-wiki The NMPDR search facility provides many different ways to look for genes, genomes, or sequences in the NMPDR database. The following searches are currently supported. {| | '''[[OpSearch]]''' || Display genes of a single genome organized into operons. |- | '''[[WordSearch]]''' || Display genes that match certain keywords. |- | '''[[FidSearch]]''' || Display genes from one or more genomes filtered by subsystem or keywords. |- | '''[[SigGenes]]''' || Display genes that are common to a set of genomes, or that differentiate between two sets of genomes. |- | '''[[ToolSearch]]''' || Search for genes or DNA using BLAST or pattern-matching. |- | '''[[SubSearch]]''' || Search for genes in a given subsystem or subsystem class. |- | '''[[DrugSearch]]''' || Show ''in silico'' docking results for select PDBs. |} The results of a search will generally start with data for the NMPDR [[core organisms]]. All NMPDR searches allow you to download results in tab-delimited and XML formats. NMPDR searches that return a list of genes also allow you to download the genes in FASTA format. Most NMPDR searches use a powerful [[Genome Control]] that allows you to choose one or more genomes according to various criteria. Some also use a search-engine style [[Keyword Box]]. The Keyword Box can also be found at the top of many of the NMPDR pages. fa29870c54b4d8171aa3918cb13fbb6a30c5430c 1670 1669 2007-07-23T20:48:47Z BruceParrello 19 An overview of the NMPDR search facility wikitext text/x-wiki The NMPDR search facility provides many different ways to look for genes, genomes, or sequences in the NMPDR database. The following searches are currently supported. {| | '''[[OpSearch]]''' || Display genes of a single genome organized into operons. |- | '''[[WordSearch]]''' || Display genes that match certain keywords. |- | '''[[FidSearch]]''' || Display genes from one or more genomes filtered by subsystem or keywords. |- | '''[[SigGenes]]''' || Display genes that are common to a set of genomes, or that differentiate between two sets of genomes. |- | '''[[ToolSearch]]''' || Search for genes or DNA using BLAST or pattern-matching. |- | '''[[SubSearch]]''' || Search for genes in a given subsystem or subsystem class. |- | '''[[DrugSearch]]''' || Show ''in silico'' docking results for select PDBs. |} The results of a search will generally start with data for the NMPDR [[core organisms]]. All NMPDR searches allow you to download results in tab-delimited and XML formats. NMPDR searches that return a list of genes also allow you to download the genes in FASTA format. Most NMPDR searches use a powerful [[Genome Control]] that allows you to choose one or more genomes according to various criteria. Some also use a search-engine style [[Keyword Box]]. The Keyword Box can also be found at the top of many of the NMPDR pages. f08fb02c8ae8b026dd8f1f06b4fdb23666c91d04 6 1423 1671 2007-07-23T21:23:19Z BruceParrello 19 A sample NMPDR search form with the blue question marks highlighted. wikitext text/x-wiki A sample NMPDR search form with the blue question marks highlighted. dc2f28b18c40231a694c6e1cbbf1f4f36cec8a6c 0 1422 1672 1670 2007-07-23T21:31:34Z BruceParrello 19 Added image and text about the hint buttons wikitext text/x-wiki The NMPDR search facility provides many different ways to look for genes, genomes, or sequences in the NMPDR database. The following searches are currently supported. {| | '''[[OpSearch]]''' || Display genes of a single genome organized into operons. |- | '''[[WordSearch]]''' || Display genes that match certain keywords. |- | '''[[FidSearch]]''' || Display genes from one or more genomes filtered by subsystem or keywords. |- | '''[[SigGenes]]''' || Display genes that are common to a set of genomes, or that differentiate between two sets of genomes. |- | '''[[ToolSearch]]''' || Search for genes or DNA using BLAST or pattern-matching. |- | '''[[SubSearch]]''' || Search for genes in a given subsystem or subsystem class. |- | '''[[DrugSearch]]''' || Show ''in silico'' docking results for select PDBs. |} The results of a search will generally start with data for the NMPDR [[core organisms]]. All NMPDR searches allow you to download results in tab-delimited and XML formats. NMPDR searches that return a list of genes also allow you to download the genes in FASTA format. Most NMPDR searches use a powerful [[Genome Control]] that allows you to choose one or more genomes according to various criteria. Some also use a search-engine style [[Keyword Box]]. The Keyword Box can also be found at the top of many of the NMPDR pages. If you have a question about something in an NMPDR search form, mouse over the blue question mark to get a hint. Click on the blue question mark to pop up the Wiki page on the subject. The blue question marks have been circled in the sample search form below. [[Image:BlueQMarks.png|Sample search form]] e9178b2269311c532209d5e6c4280bf15c3f6c48 1673 1672 2007-07-23T21:35:01Z BruceParrello 19 wikitext text/x-wiki The NMPDR search facility provides many different ways to look for genes, genomes, or sequences in the NMPDR database. The following searches are currently supported. {| | '''[[OpSearch]]''' || Display genes of a single genome organized into operons. |- | '''[[WordSearch]]''' || Display genes that match certain keywords. |- | '''[[FidSearch]]''' || Display genes from one or more genomes filtered by subsystem or keywords. |- | '''[[SigGenes]]''' || Display genes that are common to a set of genomes, or that differentiate between two sets of genomes. |- | '''[[ToolSearch]]''' || Search for genes or DNA using BLAST or pattern-matching. |- | '''[[SubSearch]]''' || Search for genes in a given subsystem or subsystem class. |- | '''[[DrugSearch]]''' || Show ''in silico'' docking results for select PDBs. |} The results of a search will generally start with data for the NMPDR [[core organisms]]. All NMPDR searches allow you to download results in tab-delimited and XML formats. NMPDR searches that return a list of genes also allow you to download the genes in FASTA format. Most NMPDR searches use a powerful [[Genome Control]] that allows you to choose one or more genomes according to various criteria. Some also use a search-engine style [[Keyword Box]]. The Keyword Box can also be found at the top of many of the NMPDR pages. If you have a question about something in an NMPDR search form, mouse over the a question mark to get a hint. Click on the blue question mark to pop up the Wiki page on the subject. The blue question marks have been circled in the sample search form below. [[Image:BlueQMarks.png|Sample search form]] 5b4a455bc06b5e3c7bb9f78537ae86d5b1914030 1674 1673 2007-07-25T21:25:53Z BruceParrello 19 Trying to fix the stupid image wikitext text/x-wiki The NMPDR search facility provides many different ways to look for genes, genomes, or sequences in the NMPDR database. The following searches are currently supported. {| | '''[[OpSearch]]''' || Display genes of a single genome organized into operons. |- | '''[[WordSearch]]''' || Display genes that match certain keywords. |- | '''[[FidSearch]]''' || Display genes from one or more genomes filtered by subsystem or keywords. |- | '''[[SigGenes]]''' || Display genes that are common to a set of genomes, or that differentiate between two sets of genomes. |- | '''[[ToolSearch]]''' || Search for genes or DNA using BLAST or pattern-matching. |- | '''[[SubSearch]]''' || Search for genes in a given subsystem or subsystem class. |- | '''[[DrugSearch]]''' || Show ''in silico'' docking results for select PDBs. |} The results of a search will generally start with data for the NMPDR [[core organisms]]. All NMPDR searches allow you to download results in tab-delimited and XML formats. NMPDR searches that return a list of genes also allow you to download the genes in FASTA format. Most NMPDR searches use a powerful [[Genome Control]] that allows you to choose one or more genomes according to various criteria. Some also use a search-engine style [[Keyword Box]]. The Keyword Box can also be found at the top of many of the NMPDR pages. If you have a question about something in an NMPDR search form, mouse over the a question mark to get a hint. Click on the blue question mark to pop up the Wiki page on the subject. The blue question marks have been circled in the sample search form below. [[Image:BlueQMarks.png]] cdc4454be6dc41818d0a0298243ee9e18c5804f5 1676 1674 2007-07-26T16:53:06Z BruceParrello 19 wikitext text/x-wiki The NMPDR search facility provides many different ways to look for genes, genomes, or sequences in the NMPDR database. The following searches are currently supported. {| | '''[[OpSearch]]''' || Display genes of a single genome organized into operons. |- | '''[[WordSearch]]''' || Display genes that match certain keywords. |- | '''[[FidSearch]]''' || Display genes from one or more genomes filtered by subsystem or keywords. |- | '''[[SigGenes]]''' || Display genes that are common to a set of genomes, or that differentiate between two sets of genomes. |- | '''[[ToolSearch]]''' || Search for genes or DNA using BLAST or pattern-matching. |- | '''[[SubSearch]]''' || Search for genes in a given subsystem or subsystem class. |- | '''[[DrugSearch]]''' || Show ''in silico'' docking results for select PDBs. |} The results of a search will generally start with data for the NMPDR [[core organisms]]. All NMPDR searches allow you to download results in tab-delimited and XML formats. NMPDR searches that return a list of genes also allow you to download the genes in FASTA format. Most NMPDR searches use a powerful [[Genome Control]] that allows you to choose one or more genomes according to various criteria. Some also use a search-engine style [[Keyword Box]]. The Keyword Box can also be found at the top of many of the NMPDR pages. If you have a question about something in an NMPDR search form, mouse over the a question mark to get a hint. Click on the blue question mark to pop up the Wiki page on the subject. The blue question marks have been circled in the sample search form below. [[Image:BlueQuestionMarks.png]] de497df7544c5ed97c94993ecfdaf51bee1b86da 1678 1676 2007-07-26T17:51:49Z BruceParrello 19 Sorted the list of search types into alphabetical order wikitext text/x-wiki The NMPDR search facility provides many different ways to look for genes, genomes, or sequences in the NMPDR database. The following searches are currently supported. {| | '''[[DrugSearch]]''' || Show ''in silico'' docking results for select PDBs. |- | '''[[FidSearch]]''' || Display genes from one or more genomes filtered by subsystem or keywords. |- | '''[[OpSearch]]''' || Display genes of a single genome organized into operons. |- | '''[[SigGenes]]''' || Display genes that are common to a set of genomes, or that differentiate between two sets of genomes. |- | '''[[SubSearch]]''' || Search for genes in a given subsystem or subsystem class. |- | '''[[ToolSearch]]''' || Search for genes or DNA using BLAST or pattern-matching. |- | '''[[WordSearch]]''' || Display genes that match certain keywords. |} The results of a search will generally start with data for the NMPDR [[core organisms]]. All NMPDR searches allow you to download results in tab-delimited and XML formats. NMPDR searches that return a list of genes also allow you to download the genes in FASTA format. Most NMPDR searches use a powerful [[Genome Control]] that allows you to choose one or more genomes according to various criteria. Some also use a search-engine style [[Keyword Box]]. The Keyword Box can also be found at the top of many of the NMPDR pages. If you have a question about something in an NMPDR search form, mouse over the a question mark to get a hint. Click on the blue question mark to pop up the Wiki page on the subject. The blue question marks have been circled in the sample search form below. [[Image:BlueQuestionMarks.png]] 62baaef2b88db85bb5f08992453e74301651db6f 6 1424 1675 2007-07-26T16:50:07Z BruceParrello 19 Highlights the blue question marks in a search form. This is a second attempt to upload this picture; I am conducting experiments to see if I can get the picture to work consistently. wikitext text/x-wiki Highlights the blue question marks in a search form. This is a second attempt to upload this picture; I am conducting experiments to see if I can get the picture to work consistently. 4c22000f3be239d62039376758aa232fdd300f7d 0 1425 1677 2007-07-26T17:49:33Z BruceParrello 19 wikitext text/x-wiki NMPDR is a [http://www.brc-central.org/cgi-bin/prok_manatee/brc-central/brc_central.cgi Bioinformatics Resource Center]. Each center specializes in certain pathogens. In NMPDR, we call these the ''core genomes'' or ''NMPDR genomes''. The genomes not in the core set are considered ''supporting genomes''. On the [[Genome Control]] and in [[NMPDR Search Results]], the core genomes are shown first. The NMPDR core genomes come from the following generae or species: * [http://www.nmpdr.org/content/campy.php Campylobacter] * [http://www.nmpdr.org/content/listeria.php Listeria] * [http://www.nmpdr.org/content/staph.php Staphylococcus aureus] * [http://www.nmpdr.org/content/strep.php Streptococcus] * [http://www.nmpdr.org/content/vibrio.php Vibrio] For some genera, such as Vibrio, the genomes are divided into subgroups by species, or by pathogenicity. These subgroups are displayed in the Genome Control. Although the core genomes are our primary focus, any complete genome for which we have reliable annotations is copied to the NMPDR as a supporting genome; however, not all of the search attributes are computed for all of the supporting genomes. Check the individual search pages (accessible from [[NMPDR Search]]) for more information about this. 5908f1fef7ff92a25dc89ee3fc566d16d87a80d2 0 1426 1679 2007-07-26T19:48:55Z BruceParrello 19 wikitext text/x-wiki One of the projects underway at the NMPDR is generating ''in silico'' docking results for proteins that are believed to be good drug targets. For each selected protein, its PDB is selected from the [http://www.rcsb.org/pdb/ Protein Data Bank] and compared against a database of over 3 million ligands taken from the [http://blaster.docking.org/zinc/ ZINC database]. For each PDB put through this process, the NMPDR selects from 55 to 60 significant results. The results are displayed on the Drug Target Search Form. Simply select a PDB in the dropdown box, and the docking energies computed for the ligands will be displayed. The energies displayed are in kcal/mol. The total energy is divided into two components: '''Van der Waals''' energy is computed by the shapes of the interlocking surfaces; '''Electrostatic''' energy is computed from the electrical attraction between the molecules. 9cbcea9c2299877a7dbfbfad6fe6d1776ac5be92 1680 1679 2007-07-28T10:02:46Z BruceParrello 19 wikitext text/x-wiki One of the projects underway at the NMPDR is generating ''in silico'' docking results for proteins that are believed to be good drug targets. For each selected protein, its PDB is selected from the [http://www.rcsb.org/pdb/ Protein Data Bank] and compared against a database of over 3 million ligands taken from the [http://blaster.docking.org/zinc/ ZINC database]. For each PDB put through this process, the NMPDR selects from 55 to 60 significant results. The results are displayed on the Drug Target Search Form. Simply select a PDB in the dropdown box, and the docking energies computed for the ligands will be displayed. The energies displayed are in kcal/mol. The total energy is divided into two components: '''Van der Waals''' energy is computed from the shapes of the interlocking surfaces; '''Electrostatic''' energy is computed from the electrical attraction between the molecules. 49afde76a42f60f139d96875167b5506f10a858b 0 1427 1681 2007-07-28T17:23:05Z BruceParrello 19 Safety save wikitext text/x-wiki An alias is a gene identifier from an outside organization or database. Inside the NMPDR's data structures, the [[FIG ID]] is used for each gene. Each gene also has a list of aliases. There may be none, or there may be a dozen. Refseq IDs are included without change, but most of the other aliases use a prefix to identify the type. The prefix ends with either a vertical bar (|) or colon (:). For example, the gene with a FIG ID of fig|100226.1.peg.3361 has the following aliases. * '''GeneID:1098838''', its Gene ID * '''gi|21221828''', its [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=Protein&list_uids=21221828&dopt=GenPept Genbank ID] * '''kegg|sco:SCO3401''', its [http://www.genome.ad.jp/dbget-bin/www_bget?sco+SCO3401 KEGG ID] * '''NP_627607.1''', its [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=protein;cmd=search;term=NP_627607.1 Refseq ID] * '''LocusTag:SCO3401''', its locus tag * '''tr|Q9X8I1''', its [http://ca.expasy.org/uniprot/Q9X8I1 TREMBL ID] * '''uni|Q9X8I1''', its [http://www.ebi.uniprot.org/uniprot-srv/uniProtView.do?proteinAc=Q9X8I1 UniProt ID] Gene names (e.g. '''dnaK''' or '''grpE'') are also considered aliases. b01229a839b5a73dca3a56e5be3d4616fe21e722 1682 1681 2007-07-28T17:33:27Z BruceParrello 19 First real version wikitext text/x-wiki An alias is a gene identifier from an outside organization or database. Inside the NMPDR's data structures, the [[FIG ID]] is used for each gene. Each gene also has a list of aliases. There may be none, or there may be a dozen. Refseq IDs are included without change, but most of the other aliases use a prefix to identify the type. The prefix ends with either a vertical bar (|) or colon (:). For example, the gene with a FIG ID of fig|100226.1.peg.3361 has the following aliases. * '''GeneID:1098838''', its Gene ID * '''gi|21221828''', its [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=Protein&list_uids=21221828&dopt=GenPept Genbank ID] * '''kegg|sco:SCO3401''', its [http://www.genome.ad.jp/dbget-bin/www_bget?sco+SCO3401 KEGG ID] * '''NP_627607.1''', its [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=protein;cmd=search;term=NP_627607.1 Refseq ID] * '''LocusTag:SCO3401''', its locus tag * '''tr|Q9X8I1''', its [http://ca.expasy.org/uniprot/Q9X8I1 TREMBL ID] * '''uni|Q9X8I1''', its [http://www.ebi.uniprot.org/uniprot-srv/uniProtView.do?proteinAc=Q9X8I1 UniProt ID] Gene names (e.g. '''dnaK''' or '''grpE''') are also considered aliases. 90b72336e4cba86aef8667307834ddb00179dc07 0 1428 1683 2007-07-28T18:19:49Z BruceParrello 19 safety save wikitext text/x-wiki The NMPDR keyword search works like a typical search engine. You type in the appropriate words, and a list of genes will come back. The keywords for a specified gene are as follows. The examples shown are for the gene '''fig|100226.1.peg.3361''', which is EC 2.7.6.3 for ''Streptomyces coelicolor A3(2)''. {| | FIG gene identifier || fig|100226.1.peg.3361 |- | The [[Alias|aliases]] || GeneID:1098838, gi|21221828, kegg|sco:SCO3401, NP_627607.1, SCO3401, tr|Q9X8I1, uni|Q9X8I1 |- | All words in the functional role || 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine, pyrophosphokinase, amino, hydroxy, hydroxymethylhydroperidine |- | The genome ID || 100226.1 |- | All words in the taxonomy || bacteria, actinobacteria, actinobacteridae, actinomycetales, streptomycineae, streptomycetaceae, streptomyces, coelicolor, a32 |- | The [[subsystem]] names and classifications || folate, biosynthesis, cofactors, vitamins, prosthetic, groups, pigments, folates, pterines |} Note that in the functional role that hyphenated words are stored in their full form as well as broken up on the hyphen boundaries. * dc3812489dd85cbc6676679dc7ddec7178c540cc 1684 1683 2007-07-28T18:33:07Z BruceParrello 19 safety save wikitext text/x-wiki The NMPDR keyword search works like a typical search engine. You type in the appropriate words, and a list of genes will come back. The keywords for a specified gene are as follows. The examples shown are for the gene '''fig|100226.1.peg.3361''', which is EC 2.7.6.3 for ''Streptomyces coelicolor A3(2)''. {| | '''FIG gene identifier''' || fig|100226.1.peg.3361 |- | '''The [[Alias|aliases]]''' || GeneID:1098838, gi|21221828, kegg|sco:SCO3401, NP_627607.1, SCO3401, tr|Q9X8I1, uni|Q9X8I1 |- | '''All words in the functional role''' || 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine, pyrophosphokinase, amino, hydroxy, hydroxymethylhydroperidine |- | '''The genome ID''' || 100226.1 |- | '''All words in the taxonomy''' || bacteria, actinobacteria, actinobacteridae, actinomycetales, streptomycineae, streptomycetaceae, streptomyces, coelicolor, a32 |- | '''The [[subsystem]] names and classifications''' || folate, biosynthesis, cofactors, vitamins, prosthetic, groups, pigments, folates, pterines |- | '''The EC number''' || 2.7.6.3 |- | '''The [[subsystem role]] || 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine, pyrophosphokinase, amino, hydroxy, hydroxymethylhydroperidine |- | '''Special Keywords''' || |} Notes * In the functional role, hyphenated words are stored in their full form (''2-amino-4-hydroxy-6-hydroxymethyldihydropteridine'') as well as broken up on the hyphen boundaries ('''amino- hydroxy hydroxymethyldihydropteridine'''). * The subsystem role for this gene is the same as the functional role. * Keywords are case-insensitive * Special keywords 52f025b92b9e7de59dc4d1232354f5fba9c9cc99 1685 1684 2007-07-28T19:10:43Z BruceParrello 19 Changed to a more complicated example gene wikitext text/x-wiki The NMPDR keyword search works like a typical search engine. You type in the appropriate words, and a list of genes will come back. The keywords for a specified gene are as follows. The examples shown are for the gene '''fig|171101.1.peg.269''', which is sulD for ''Streptococcus pneumoniae R6''. {| | '''FIG gene identifier''' || fig|171101.1.peg.269 |- | '''The [[Alias|aliases]]''' || GeneID:934668, gi|15902313, kegg|spd:SPD_0272, kegg|spr:spr0269, NP_357863.1, sp|P59657, spr0269, sulD, tr|Q04MF8, uni|P59657, uni|Q04MF8 |- | '''All words in the functional role''' || Dihydroneopterin, aldolase 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine, pyrophosphokinase amino, hydroxy, hydroxymethyldihydropteridine |- | '''The genome ID''' || 171101.1 |- | '''All words in the taxonomy''' || bacteria, firmicutes, lactobacillales, streptococcaceae, streptococcus, pneumoniae, r6 |- | '''The [[subsystem]] names and classifications''' || folate, biosynthesis, cofactors, vitamins, prosthetic, groups, pigments, folates, pterines |- | '''The EC number''' || 2.7.6.3, 4.1.2.25 |- | '''The [[subsystem role]] || 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine, pyrophosphokinase, amino, hydroxy, hydroxymethylhydroperidine |- | '''Special Keywords''' || essential |} Notes * In the functional role, hyphenated words are stored in their full form (''2-amino-4-hydroxy-6-hydroxymethyldihydropteridine'') as well as broken up on the hyphen boundaries ('''amino- hydroxy hydroxymethyldihydropteridine'''). * Keywords are case-insensitive * Special keywords indicate attributes of the gene. The list of special keywords currently supported appears below. ** ''virulence'', which indicates the gene participates in the process of helping the organism to damage its host ** ''essential'', which indicates that the gene is essential to to the survival of the organism ** ''iedb'', which indicates that the gene is listed in the [http://www.immuneepitope.org/home.do Immune Epitope Database] 73c432a5c34d0c98b36e6799cdcc5bd511f0e0ce 1686 1685 2007-07-28T20:05:44Z BruceParrello 19 safety save wikitext text/x-wiki The NMPDR keyword search works like a typical search engine. You type in the appropriate words, and a list of genes will come back. Our keyword database contains millions of words, including ''vitamins'', ''aldolase'', and ''pyrophosphokinase''. The NMPDR looks at nine specific data items when computing the keywords for a gene. The table below shows each of the nine steps along with the keywords derived by that step for the gene '''fig|171101.1.peg.269''', a dual-role protein encoding gene for ''Streptococcus pneumoniae r6'' that has 40 keywords. {| | '''FIG gene identifier''' || fig|171101.1.peg.269 |- | '''The [[Alias|aliases]]''' || GeneID:934668, gi|15902313, kegg|spd:SPD_0272, kegg|spr:spr0269, NP_357863.1, sp|P59657, spr0269, sulD, tr|Q04MF8, uni|P59657, uni|Q04MF8 |- | '''All words in the functional role''' || Dihydroneopterin, aldolase 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine, pyrophosphokinase amino, hydroxy, hydroxymethyldihydropteridine |- | '''The genome ID''' || 171101.1 |- | '''All words in the taxonomy''' || bacteria, firmicutes, lactobacillales, streptococcaceae, streptococcus, pneumoniae, r6 |- | '''The [[subsystem]] names and classifications''' || folate, biosynthesis, cofactors, vitamins, prosthetic, groups, pigments, folates, pterines |- | '''The EC number''' || 2.7.6.3, 4.1.2.25 |- | '''The [[subsystem role]] || 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine, pyrophosphokinase, amino, hydroxy, hydroxymethylhydroperidine |- | '''Special Keywords''' || essential |} ====Notes==== * Some keywords appear twice. * In the functional role, hyphenated words are stored in their full form (''2-amino-4-hydroxy-6-hydroxymethyldihydropteridine'') as well as broken up on the hyphen boundaries ('''amino- hydroxy hydroxymethyldihydropteridine'''). * Keywords are case-insensitive * Special keywords indicate attributes of the gene. Most of these are incomplete: for example, we know certain genes are virulence-associated, but for most of the genes we have no virulence data. ** ''virulence'', which indicates the gene participates in the process of helping the organism to damage its host. This attribute is incomplete. ** ''essential'', which indicates that the gene is essential to to the survival of the organism. This attribute is incomplete. ** ''iedb'', which indicates that the gene is listed in the [http://www.immuneepitope.org/home.do Immune Epitope Database] ===Advanced Keyword Searching=== Normally, the search process selects the genes relevant to all the words in the keyword box. You can modify the default behavior by prefixing control characters to the keywords. {| |Char|Meaning|Example|Explanation of Example |- |'''-'''|negation|'''2.7.6.3 -firmicutes''': search for all genes with EC number 2.7.6.3 that are not in firmicutes |- |'''()'''|optional| 55e0fda471ac06ecb438d8505b475223b0230402 1687 1686 2007-07-28T20:51:53Z BruceParrello 19 First real version wikitext text/x-wiki The NMPDR keyword search works like a typical search engine. You type in the appropriate words, and a list of genes will come back. Our keyword database contains millions of words, including ''vitamins'', ''aldolase'', and ''pyrophosphokinase''. The NMPDR looks at nine specific data items when computing the keywords for a gene. The table below shows each of the nine steps along with the keywords derived by that step for the gene '''fig|171101.1.peg.269''', a dual-role protein encoding gene for ''Streptococcus pneumoniae r6'' that has 40 keywords. {|border="2" | '''FIG gene identifier''' || fig|171101.1.peg.269 |- | '''The [[Alias|aliases]]''' || GeneID:934668, gi|15902313, kegg|spd:SPD_0272, kegg|spr:spr0269, NP_357863.1, sp|P59657, spr0269, sulD, tr|Q04MF8, uni|P59657, uni|Q04MF8 |- | '''All words in the functional role''' || Dihydroneopterin, aldolase 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine, pyrophosphokinase amino, hydroxy, hydroxymethyldihydropteridine |- | '''The genome ID''' || 171101.1 |- | '''All words in the taxonomy''' || bacteria, firmicutes, lactobacillales, streptococcaceae, streptococcus, pneumoniae, r6 |- | '''The [[subsystem]] names and classifications''' || folate, biosynthesis, cofactors, vitamins, prosthetic, groups, pigments, folates, pterines |- | '''The EC number''' || 2.7.6.3, 4.1.2.25 |- | '''The [[subsystem role]] || 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine, pyrophosphokinase, amino, hydroxy, hydroxymethylhydroperidine |- | '''Special Keywords''' || essential |} ====Notes==== * Some keywords appear twice. * In the functional role, hyphenated words are stored in their full form (''2-amino-4-hydroxy-6-hydroxymethyldihydropteridine'') as well as broken up on the hyphen boundaries ('''amino hydroxy hydroxymethyldihydropteridine'''). * Keywords are case-insensitive * Special keywords indicate attributes of the gene. Most of these are incomplete: for example, we know certain genes are virulence-associated, but for most of the genes we have no virulence data. ** ''virulence'', which indicates the gene participates in the process of helping the organism to damage its host. This attribute is incomplete. ** ''essential'', which indicates that the gene is essential to to the survival of the organism. This attribute is incomplete. ** ''iedb'', which indicates that the gene is listed in the [http://www.immuneepitope.org/home.do Immune Epitope Database] ===Advanced Keyword Searching=== Normally, the search process selects the genes relevant to all the words in the keyword box. You can modify the default behavior using the following control characters. {|border="2" | '''char''' || '''Meaning''' || '''Example''' || '''Explanation of Example''' |- | '''-''' || negation || 2.7.6.3 '''-'''firmicutes || search for all genes with EC number 2.7.6.3 that are not in firmicutes |- | '''()''' || optional || '''('''2.7.6.3 4.1.2.25''')''' || search for any gene with EC number 2.7.6.3 or 4.1.2.25 |- | '''""''' || phrase || '''"'''folate biosynthesis'''"''' || search for all genes that participate in folate biosynthesis |} 43fe2941d82115148f32df2c72691dee12427b98 1688 1687 2007-07-29T19:17:10Z BruceParrello 19 Added notes on using negation wikitext text/x-wiki The NMPDR keyword search works like a typical search engine. You type in the appropriate words, and a list of genes will come back. Our keyword database contains millions of words, including ''vitamins'', ''aldolase'', and ''pyrophosphokinase''. The NMPDR looks at nine specific data items when computing the keywords for a gene. The table below shows each of the nine steps along with the keywords derived by that step for the gene '''fig|171101.1.peg.269''', a dual-role protein encoding gene for ''Streptococcus pneumoniae r6'' that has 40 keywords. {|border="2" | '''FIG gene identifier''' || fig|171101.1.peg.269 |- | '''The [[Alias|aliases]]''' || GeneID:934668, gi|15902313, kegg|spd:SPD_0272, kegg|spr:spr0269, NP_357863.1, sp|P59657, spr0269, sulD, tr|Q04MF8, uni|P59657, uni|Q04MF8 |- | '''All words in the functional role''' || Dihydroneopterin, aldolase 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine, pyrophosphokinase amino, hydroxy, hydroxymethyldihydropteridine |- | '''The genome ID''' || 171101.1 |- | '''All words in the taxonomy''' || bacteria, firmicutes, lactobacillales, streptococcaceae, streptococcus, pneumoniae, r6 |- | '''The [[subsystem]] names and classifications''' || folate, biosynthesis, cofactors, vitamins, prosthetic, groups, pigments, folates, pterines |- | '''The EC number''' || 2.7.6.3, 4.1.2.25 |- | '''The [[subsystem role]] || 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine, pyrophosphokinase, amino, hydroxy, hydroxymethylhydroperidine |- | '''Special Keywords''' || essential |} ====Notes==== * Some keywords appear twice. * In the functional role, hyphenated words are stored in their full form (''2-amino-4-hydroxy-6-hydroxymethyldihydropteridine'') as well as broken up on the hyphen boundaries ('''amino hydroxy hydroxymethyldihydropteridine'''). * Keywords are case-insensitive. * Special keywords indicate attributes of the gene. Most of these are incomplete: for example, we know certain genes are virulence-associated, but for most of the genes we have no virulence data. ** ''virulence'', which indicates the gene participates in the process of helping the organism to damage its host. This attribute is incomplete. ** ''essential'', which indicates that the gene is essential to to the survival of the organism. This attribute is incomplete. ** ''iedb'', which indicates that the gene is listed in the [http://www.immuneepitope.org/home.do Immune Epitope Database] ===Advanced Keyword Searching=== Normally, the search process selects the genes relevant to all the words in the keyword box. You can modify the default behavior using the following control characters. {|border="2" | '''char''' || '''Meaning''' || '''Example''' || '''Explanation of Example''' |- | '''-''' || negation || 2.7.6.3 '''-'''firmicutes || search for all genes with EC number 2.7.6.3 that are not in firmicutes |- | '''()''' || optional || '''('''2.7.6.3 4.1.2.25''')''' || search for any gene with EC number 2.7.6.3 or 4.1.2.25 |- | '''""''' || phrase || '''"'''folate biosynthesis'''"''' || search for all genes that participate in folate biosynthesis |} ===Using Negation=== It is illegal to use negation on all the keywords. For example, you can't do -hypothetical to get all non-hypothetical proteins. You can trick the the keyword search a little by including a positive keyword for a broad category bacteria -hypothetical which will return all non-hypothetical proteins for bacteria. This is not recommended, however, because you will get over a million results. Queries that rely primarily on negation make the most sense when your result set is already restricted. ee23d163f90f8ebbb7e0e3f6e08f40f2b1b6a00e 6 1429 1689 2007-07-30T23:14:17Z BruceParrello 19 NMPDR Genome selection control wikitext text/x-wiki NMPDR Genome selection control 649a26db9ebe3691cdcc565470e74beb94f55fa6 0 1430 1690 2007-07-31T21:39:14Z BruceParrello 19 Safety save wikitext text/x-wiki The Genome Control is a powerful tool for selecting one or more genomes. It lists every genome available in the NMPDR, sorted by [[species group]] and color-coded by domain. Bacteria are shaded light pink, archaea are light blue, and eukaryota are yellow. The species groups for the NMPDR [[core organisms]] are placed at the top, and the other genes are shown at the bottom, separated by domain. [[Image:GenomeControl.png]] The genome list is a classic HTML list control. Clicking a genome selects it and deselects all others. Use CTRL-click to toggle individual genomes and SHIFT-click to select a range of genomes. At the bottom of the control is a list of the genomes you've selected. Since the list box only shows a small number of genomes at a time, the Select 05bec325ebb4bff5e196431c5287bd648451926d 1691 1690 2007-07-31T22:45:37Z BruceParrello 19 First real version wikitext text/x-wiki The Genome Control is a powerful tool for selecting one or more genomes. It lists every genome available in the NMPDR, sorted by [[species group]] and color-coded by domain. Bacteria are shaded light pink, archaea are light blue, and eukaryota are yellow. The species groups for the NMPDR [[core organisms]] are placed at the top, and the other genes are shown at the bottom, separated by domain. [[Image:GenomeControl.png]] The genome list is a classic HTML list control. Clicking a genome selects it and deselects all others. Use CTRL-click to toggle individual genomes and SHIFT-click to select a range of genomes. Below the genome list is a text box and a long button labeled '''Select genomes containing'''. This is called the ''Instant Search Bar''. Put any string in the text box, click the '''Select genomes containing''' button, and each genome with the specified string in its name will be selected. The string you type can be a genus name, a species name, a unique characterization, or a taxonomy number. In the box above, the two genomes shown were selected by typing '''vulnificus'''. Typing '''Vibrio''' would select all Vibrio genomes. Typing '''83333''' would select ''E Coli K12''. Genome selection by this method is always additive: in other words, if you typed '''strep''' into the text box in the situation shown above, as it is shown above the ''Vibrio vulnificus'' genomes would remain selected. To start from scratch with a blank list, click the '''Clear All''' button. Below the Instant Search Bar are three special-purpose buttons. * '''Clear All''' deselects all the genomes. * '''Select All''' selects all the genomes. * '''Select NMPDR''' selects all NMPDR [[core organisms]] and deselects the others. At the bottom of the control is a list of the genomes you've selected. The list box only shows a small number of genomes at a time, but the Selected-Genomes display will always include the complete list of genomes selected. bc9e64160389fa93a29733487810e9848099cc02 0 1431 1692 2007-07-31T22:56:01Z BruceParrello 19 First version wikitext text/x-wiki A species group is a group of related organisms in the NMPDR. There are specific groups for the NMPDR [[core organisms]]. The remaining organisms are in a single group. Sometimes this latter group is referred to as the ''supporting group''. In the [[Genome Control]], the supporting organisms are split by domain. In the [[NMPDR Search Results]], the core organisms are shown first and the supporting group is shown below that. a69b3fa6af79232db1b453e472fcd16cd84ced0b 0 1369 1693 1515 2007-08-07T20:37:08Z FolkerMeyer 2 Added date and fixed typo in Palsson wikitext text/x-wiki '''A manifesto written in early 2004.''' The Project to Annotate the First 1000 Sequenced Genomes, Develop Detailed Metabolic Reconstructions, and Construct the Corresponding Stoichiometric Matrices by Ross Overbeek === Introduction === In December, 2003 The Fellowship for Interpretation of Genomes (FIG) initiated The Project to Annotate 1000 Genomes (P1K). The explicit goal was to develop a technology for more accurate, high-volume annotation of genomes and to use this technology to provide superior annotations for the first 1000 sequenced genomes. Members of FIG were convinced that the current approaches for high-throughput annotation, based on protein families and automated pipelines that processed genomes sequentially, would ultimately fail to produce annotations of the desired accuracy. We believe that the key to development of high-throughput annotation technology is to have experts annotate single subsystems over the complete collection of genomes. The existing annotation approaches, in which teams analyze a whole genome at a time, ensure that annotators have no special expertise relating to the vast majority of genes they annotate. By having individuals annotate single subsystems over a large collection of genomes, we allow individuals with expertise in specific pathways (or, more generally, subsystems) to perform their task with relatively high accuracy. The early stages of the effort began at FIG, but quickly spread to a number of cooperating institutions, most notably Argonne National Lab. During the first year of the project, we have developed detailed encodings of subsystems that include a majority of the genes from subsystems that make up the core cellular machinery. More importantly, we have developed the initial versions of technology needed to support the project. The Project to Annotate 1000 Genomes has reached the stage where it is clear that it will very shortly produce what we call informal metabolic reconstructions that cover the majority of central metabolism as it is implemented in the close to 300 more-or-less complete genomes that are now available. We think of an informal metabolic reconstruction as a partitioning of the cellular machinery into subsystems, the specification of the functional roles that make up each subsystem, and the inventory of which genes in a specific organism implement the functional roles. What is needed to support both qualitative analysis and effective quantitative modeling is to convert these informal metabolic reconstructions into formal metabolic reconstructions. By a formal reconstruction, we mean an accurate encoding of the metabolic network. The goal of such an encoding is to construct a list of metabolites and a detailed reaction network that is internally consistent (in the sense that metabolites that are produced by reactions are connected as substrates to other reactions or to specific transporters, and that all metabolites that act as substrates are produced by other reactions or provided by transporters). Perhaps, a better way to put this is that all apparent anomalies are highlighted as such, and the essential components of the metabolic network are accurately encoded. The output of such an effort is normally what is termed a stoichiometric matrix, the basic resource required to support stoichiometric modeling. One of the central goals of this enlarged effort is to develop accurate stoichiometric matrices for each of the 1000 genomes; we refer to this component of the effort as The Project to Produce 1000 Stoichiometric Matrices. It is our belief that the development of the technology required to mass-produce accurate genome annotations will ultimately allow fully automated annotation pipelines to achieve relatively high accuracy. Similarly, the existence of 1000 accurate formal metabolic reconstructions would constitute a resource that would allow rapid and accurate development of stoichiometric matrices for newly-sequenced genomes. That is, besides producing accurate annotations, informal metabolic reconstructions, formal metabolic reconstructions, and stoichiometric matrices for a large collection of diverse genomes, we believe that the expanded project will produce technology that will support nearly automatic, very rapid characterization of new genomes. All of the encoded subsystems, metabolic reconstructions and stoichiometric matrices will be made freely available on open web sites. In addition, the software environments used to develop the encoded subsystems and stoichiometric matrices will be developed and supported as open source software. By making the fundamental data items, the encoded subsystems and stoichiometric matrices, freely available to the community, we expect to stimulate development of alternative software systems to support curation and maintenance of these items. === The Project to Annotate 1000 Genomes === We have chosen to conceptually break the Project to Annotate 1000 Genomes into three stages. We discuss these stages as if they will occur sequentially; in fact, all three stages are now in progress. To understand the three stages, the reader must have at least a rudimentary grasp of what we mean by an encoded subsystem and an informal metabolic reconstruction. When we speak of a subsystem, we think of a set of related functional roles. In a specific organism, a set of genes implement these roles, and we think of those genes as constituting the subsystem in that organism. That is, we are really dealing with an abstract notion of subsystem (in which the subsystem is a set of functional roles) and instances of the subsystem in a specific organism (in which a set of genes implements the abstract functional roles). Precisely the same subsystem and functional roles exist in distinct organisms, although obviously the genes are unique to each organism. Subsystems are thought of as possibly having multiple variants. Organisms that have operational versions of a subsystem may well have genes that implement slightly different subsets of the functional roles that make up the subsystem. Each subset of functional roles that exists in at least one organism with an operational version of the subsystem constitutes an operational variant. We think of an informal metabolic reconstruction for an organism as a set of operational variants of subsystems that are believed to exist for the organism. In this conceptualization, one does not have a meaningful functional hierarchy or DAG; rather, we simply have an inventory of functional roles that are implemented in the organism, along with the variants of subsystems that they implement. We do believe that the task of imposing an actual hierarchy is relatively straightforward in comparison with the effort required to construct the set of operational variants. In some contexts, we have included a functional overview in which the subsystems are embedded at the lowest levels. It is clear that, given a diverse collection of informal metabolic reconstructions, the development of appropriate functional hierarchies can be generated with relatively few resources. Our encoding of a subsystem can now be reduced to a specification of a set of functional roles (this amounts to the abstract subsystem) and sets of genes which implement the operational variants in a number of genomes. These genes are given as a subsystem spreadsheet in which each row corresponds to a single genome, each column corresponds to a single functional role, and each cell contains the set of genes in that genome that are believed to implement the given functional role. The Project to Annotate 1000 Genomes amounts to an effort to produce detailed and comprehensive encodings of several hundred subsystems, which will impose assigned functions on genes in each of the genomes. The total percent of genes that can be assigned functions this way is probably on the order of 50-70% in most genomes (in large eukaryotic genomes the total is obviously substantially lower). The percent will grow as our understanding grows. What should be noted is that the accuracy of these assignments will be substantially better than that of current assignments, and the conserved cellular machinery almost all falls within the projected subsystems. Once we have produced our initial set of annotations, we believe that automated pipelines and protein families are excellent tools for propagating them. Protein families are, in fact, a key component of annotation and provide the fundamental mechanism for projection of function between genes. The added dimension provided by subsystems, along with the manual curation required to develop accurate initial encodings of subsystems, is an essential technology for increasing the accuracy and effectiveness of protein families. Ultimately the encoded subsystems will be used to make incremental, essential corrections to collections of protein families (like those supported by UniProt and COGs), and a basis for much more accurate annotation will emerge. === We now proceed to describe the details of the three stages. === ==== Stage 1: Development of Initial Encodings of Subsystems ==== The initial stage of the project will involve development of approximately 100-150 subsystems that will cover most of the conserved cellular machinery in prokaryotes (and all of the central metabolic machinery in eukaryotes). This work will be done largely by trained annotators who achieve a limited mastery of specific subsystems via review articles and detailed analysis of the collection of genomes. These individuals can define the abstract subsystems and add most genomes to the emerging spreadsheets, but not without error. They are necessarily far less skilled than experts who have invested tens of years in study of specific subsystems. These initial subsystems will have many uses. They can be used to enhance sets of curated protein families, to clarify identification of gene starts, and to develop a consistent set of annotations. They will form the basis of informal metabolic reconstructions, and will be used to support the development of formal metabolic reconstructions. However, given the relative lack of expertise of these initial annotators and the fact that they will seldom have access to the wet lab facilities needed to remove ambiguities in assignments, errors will inevitably remain. ==== Stage 2: The Use of True Experts and the Wet Lab to Refine the Encodings ==== The second stage will involve the gradual refinement and enhancement of the original subsystem encodings by domain experts. Almost every subsystem spreadsheet makes it clear that numerous detailed questions remain to be answered. These questions relate to correcting gene calls, correction of frameshifts, refining function assignments, and removing ambiguities (either via bioinformatics based analysis or through actual wet lab efforts). The participation of domain experts will be critical, but it seems most likely that a relatively small set will choose to get involved until the utility of the approach becomes obvious. We already have some domain experts (in translation, transcription, and a limited number of metabolic subsystems) participating in the effort. We believe that this number will grow rapidly over the next 2-3 years. It should be emphasized that upon completion of step 2 we will have accurate annotations and a solid foundation for the construction of stoichiometric matrices. ==== Stage 3: Understanding the Evolutionary History of the Genes within the Subsystem ==== The third stage involves determination of the evolutionary history of the genes within the subsystem. To understand what this involves and the utility of this type of analysis, we must simply recommend two papers by the team led by Roy Jensen: Ancient origin of the tryptophan operon and the dynamics of evolutionary change by Xie, Keyhani, Bonner, Jensen, Microbiol Mol Biol Rev. 2003 Sep;67(3):303-42 Inter-genomic displacement via lateral transfer of bacterial trp operons in an overall context of vertical genealogy, by Xie, Song, Keyhani, Bonner, Jensen, BMC Biology, 2004, 2:15 These papers elegantly display the exact style of analysis required to uncover and clarify the evolutionary history of the relevant genes. Essentially, trees must be built containing all of the genes implementing each specific functional role (multiple trees may be needed for distinct forms). Those trees that display a common topology indicate which columns in the spreadsheet can be used to infer the most probable vertical history of the subsystem. Once the overall history has been clarified, it becomes possible to attempt clarification of horizontal transfers, to reconstruct the history of clusters on the chromosome, and in some cases to tie the analysis to regulatory issues. The effort required to do this style of analysis well is high. While we expect the initial efforts to go slowly, we also expect experience and advances in tools to dramatically reduce the required effort. In any event, it is clear that this stage will not be completed in the next few years, but will undoubtedly stimulate large amounts of related research. === Filling in the Missing Pieces === The encoded subsystems produced by the Project to Annotate 1000 Genomes offer a detailed picture of exactly what components have been identified and are present in each genome. Perhaps as significant, they vividly display exactly what is missing or ambiguous, allowing one to arrive at an accurate inventory of gaps in our understanding. The issue of how best to address these gaps is an integral part of the project. The technology that is emerging is what we refer to as the bioinformatics-driven wet lab. This concept refers to the development of a wet lab that utilizes conventional biochemical and genetic techniques in a framework designed to maximize the overall number of confirmations. It is driven by predictions arising from the analysis of subsystems, and it targets a prioritized list of conjectures. That is, the explicit goal is to fill in as many gaps and remove as many ambiguities as possible for resources consumed. Although it is inconceivable that one experimental group would be able to assess all of the functional predictions, we believe that integrating an experimental component into our annotation/modeling effort will directly support our main goal. In addition to verification of key predictions and removal of central ambiguities, it will validate the overall approach and set an example for other groups worldwide. === The Project to Develop 1000 Stoichiometric Matrices === We believe that the informal metabolic reconstructions are of substantial value by themselves. Indeed, numerous applications are quite obvious. However, they are not enough to support quantitative modeling. Whole genome modeling will require development of stoichiometric matrices, an effort that will pay many dividends. The most immediate payout is as quality control on the informal metabolic reconstruction. Just as the use of subsystems imposes a critical set of consistency checks on the assignment of function to genes, an attempt to develop an internally consistent reaction network imposes a strong consistency check on both the annotations and assertions of the presence of specific subsystems. Over the last 4-5 years, the success of stoichiometric modeling has set the stage for large-scale employment of the technology. The key limiting factor is the development of the stoichiometric matrix itself. This is a time-consuming task that frequently requires on the order of a year for a skilled practitioner. Many actual modeling efforts have foundered on just the technical difficulties in producing this basic datum. Bernhard Palsson has pioneered much of the key research that has led to the recent successes. Spending large amounts of effort, his team has built a very few of these stoichiometric matrices, iteratively improving their accuracy. They have successfully used these matrices to support initial modeling efforts on the organisms, and the results have gained international recognition. Palsson's team originated the The Project to Produce 1000 Stoichiometric Matrices, and they will play the lead role in converting the informal metabolic reconstructions into formal reconstructions and produce the matrices. The team at FIG and Argonne National Laboratory will participate in the effort, coordinating closely with Palsson's team. At this point, the Palsson team and the teams at FIG, ANL, and The Burnham Institute are all working on issues relating to tools to automate the generation of matrices from informal metabolic reconstructions. === The Participants === We expect participants in both projects from many institutions worldwide, probably with both academic and commercial interests. Initially, it is likely that the effort will be led from FIG, ANL and Palsson's team at UCSD. We are planning on Roy Jensen playing a role relating to quality control and development of tools to support Stage 3 analysis. Andrei Osterman from the Burnham Institute will lead wet lab efforts to challenge in silico predictions. If the effort is successful, we would hope to stimulate numerous research efforts worldwide, and we welcome broad participation. Ultimately, leadership and participation will broaden rapidly, if the effort is successful. === A Proposed Schedule === Let us begin by estimating the point at which 1000 genomes will become available. One simple approach would go as follows: The number of genomes will double approximately every 18 months. We now have about 300 more-or-less complete genomes. Therefore, we should have approximately 1000 genomes in just a bit under 3 years (by sometime in 2007) There is a great deal in this analysis that is far from certain. However, let us use this estimate as a working hypothesis. ==== 2005 ==== During 2005, Stage 1 will be completed for the vast majority of subsystems. Stage 2 will be initiated for 30-50 subsystems. Less than 10 will move deeply into stage 3. We will actively attempt to produce 10-15 stoichiometric matrices. We will focus on diverse organisms of interest to DOE and a set of gram-positive pathogens. We will begin a detailed review for quality assurance by a small number of expert biochemists and microbiologists. We expect wet lab confirmations to begin, but this is one area in which funding plays an essential role. We expect funding to support targeted confirmation/rejection of the numerous conjectures arising from the bioinformatics to begin in 2005-2006. It is possible to fairly accurately predict the potential flow of confirmations, but we cannot predict available funding. We believe that the bioinformatics-driven wet lab, in which conjectures are prioritized and grouped, would allow a relatively small group (of 3-4 postdocs and technician) to characterize up to 50 novel gene families encoding the most important functional roles in central metabolic subsystems of diverse organisms per year. ==== 2006 ==== During 2006, the vast majority of subsystems will enter Stage 2. We will attempt to move a large number into Stage 3 (this is truly difficult to predict; it depends hugely on success with the early attempts, our ability to reduce the required effort, and the research aims of the participants). We would plan on completing at least 200 more stoichiometric matrices. If the wet lab component of the effort is fully functional, we would expect a steady stream of confirmations, and (based on our past experience) we would project roughly that 75-90% of the tested conjectures will be validated. ==== 2007 ==== During 2007 we would plan on pushing Stage 2 and 3 analysis as far as possible. We believe that we will have the subsystems needed to cover the vast majority of well understood subsystems and many that are not well understood. We would plan on completing initial stoichiometric matrices for several hundred more genomes. Since the majority of the genomes will not become available until this year, of necessity many of the stoichiometric matrices will not be reasonably complete before sometime in 2008 or 2009. If the wet lab component of the effort is fully functional, we would expect the stream of successful conjectures to stimulate numerous labs to join the effort. Ultimately, the role of the wet lab component that is tightly-coupled to the project is to demonstrate the huge improvement in efficiency that can be attained by coupling the wet lab effort to well-chosen, targeted conjectures generated from the subsystems. === A Short Note on the Analysis of Environmental Samples === It is becoming clear that analysis of environmental samples will become increasingly significant. Consider a framework in which we have 1000 genomes and detailed informal metabolic reconstructions for all of them. We believe that, given a substantial environmental sample, it will be possible to produce accurate estimates of which organisms are present (where an "organism" in this context should probably be viewed as "some organism within a very constrained phylogenetic neighborhood"), it will be possible to produce fairly precise estimates of the metabolism of the organisms believed to be present, and it will be possible to compared the predicted metabolism with the actual enzymes detected in the environmental sample. The hope is clearly that we will be able to make accurate estimates, given 1000 well-annotated genomes. == Summary == The value of a collection of 1000 genomes depends directly on the quality of the annotations, the corresponding metabolic reconstructions, and the extent to which the foundations of modeling have been established. The Project to Annotate 1000 Genomes is based directly on the notion of building a collection of carefully created and curated subsystems. The fact that the individuals who encode these subsystems annotate the same subsystem over a broad collection of genomes allows them to gain an understanding of detailed variation and at least a minimal grasp of the review literature. They will be annotating genes for which they develop some detailed familiarity. We place this technology in direct opposition to the existing approaches in which individuals annotate complete genomes (assuring an almost complete lack of familiarity with the majority of genes being annotated), and automated pipelines are badly limited by the ambiguities and errors in existing annotations. The Project to Produce 1000 Stoichiometric Matrices has the potential of laying the foundations for quantitative modeling. Many, if not most, existing modeling efforts are dramatically hampered by the fact that very, very few stoichiometric matrices now exist, and the cost of developing more using existing approaches is quite high. The development of a wet lab component that challenges a carefully prioritized set of conjectures flowing from both the subsystems analysis and the initial modeling based on quantitative modeling is essential. It will confirm the relative efficiency of this approach (which might reasonably be characterized as "picking the low-hanging fruit"), and in the process establish a paradigm that directly challenges the more common approach to establishing priorities. We claim to understand the key technology needed to develop high-throughput development of annotations, metabolic reconstructions, and stoichiometric matrices. By the summer of 2005, this should be completely obvious. 02674224405c15a29da212dcadec5303deb42ccc 0 1432 1694 2007-08-15T16:23:10Z TobiasPaczian 17 wikitext text/x-wiki == Numbers in the SeedViewer, RAST Server and MG-RAST Server == The SeedViewer offers you a large number of statistics and detailed numbers about your organism. The purpose of this page is to explain how we calculate these numbers and what they mean. === MG-RAST === On the details page of your organism, you will find the following numbers: * ''Number of sequences'' : This is the total number of sequences submitted by the user for this genome. Not all of these will produce results later on. It is possible and very probable that some sequences can not be matched to anything in our database. * ''Total sequence length'' : This is the sum of the lengths of all submitted sequences. * ''Average read length'' : This is the '''Total sequence length''' divided by the '''Number of sequences''' * ''Longest sequence id' : * ''Longest sequence length'' : * ''Shortest sequence id'' : * ''Shortest sequence length'' : 3e69f7945460534ffcfb1a3db1d4f4ae5fdd48c2 1695 1694 2007-08-15T16:23:32Z TobiasPaczian 17 /* Numbers in the SeedViewer, RAST Server and MG-RAST Server */ wikitext text/x-wiki = Numbers in the SeedViewer, RAST Server and MG-RAST Server = The SeedViewer offers you a large number of statistics and detailed numbers about your organism. The purpose of this page is to explain how we calculate these numbers and what they mean. === MG-RAST === On the details page of your organism, you will find the following numbers: * ''Number of sequences'' : This is the total number of sequences submitted by the user for this genome. Not all of these will produce results later on. It is possible and very probable that some sequences can not be matched to anything in our database. * ''Total sequence length'' : This is the sum of the lengths of all submitted sequences. * ''Average read length'' : This is the '''Total sequence length''' divided by the '''Number of sequences''' * ''Longest sequence id' : * ''Longest sequence length'' : * ''Shortest sequence id'' : * ''Shortest sequence length'' : 57b194709330249b03d334b29ff0eb16da661cfe 1696 1695 2007-08-15T16:24:15Z TobiasPaczian 17 /* Numbers in the SeedViewer, RAST Server and MG-RAST Server */ wikitext text/x-wiki The SeedViewer, RAST-Server and MG-RAST-Server offer you a large number of statistics and detailed numbers about your organism. The purpose of this page is to explain how we calculate these numbers and what they mean. === MG-RAST === On the details page of your organism, you will find the following numbers: * ''Number of sequences'' : This is the total number of sequences submitted by the user for this genome. Not all of these will produce results later on. It is possible and very probable that some sequences can not be matched to anything in our database. * ''Total sequence length'' : This is the sum of the lengths of all submitted sequences. * ''Average read length'' : This is the '''Total sequence length''' divided by the '''Number of sequences''' * ''Longest sequence id' : * ''Longest sequence length'' : * ''Shortest sequence id'' : * ''Shortest sequence length'' : ca4329909d373ae45da8165d9e796e95f4e49824 1697 1696 2007-08-15T16:33:06Z TobiasPaczian 17 /* MG-RAST */ wikitext text/x-wiki The SeedViewer, RAST-Server and MG-RAST-Server offer you a large number of statistics and detailed numbers about your organism. The purpose of this page is to explain how we calculate these numbers and what they mean. === MG-RAST === On the details page of your organism, you will find the following numbers: * ''Number of sequences'' : This is the total number of sequences submitted by the user for this genome. Not all of these will produce results later on. It is possible and very probable that some sequences can not be matched to anything in our database. * ''Total sequence length'' : This is the sum of the lengths of all submitted sequences. * ''Average read length'' : This is the '''Total sequence length''' divided by the '''Number of sequences''' * ''Longest sequence id' : This is the identifier string of the longest sequence submitted. * ''Longest sequence length'' : This is the length of the longest sequence submitted. * ''Shortest sequence id'' : This is the identifier string of the shortest sequence submitted. * ''Shortest sequence length'' : This is the length of the shortest sequence submitted === RAST === On the details page of your organism, you will find the following numbers: * ''Number of features'' : This is the number of features the RAST-Server could identify in your uploaded genome and match to our database. * ''Number of warnings'' : This is the number of warnings issued by the pipeline while processing your genome. This refers to inconsistencies detected, which are not fatal to annotation, but which should be investigated further. The numbers for each type of warnings are listed below. * ''Number of fatal problems'' : This is the number of problems which cause the pipeline to be unable to process your genome. These problems have to be addressed before the annotation process can finish. * ''Possibly missing genes'' : * ''Convergent overlaps'' : * ''Divergent overlaps'' : * ''Same strand overlaps'' : === SeedViewer === On the ''Organism Overview'' page, there are a number of statistical counts about the selected genome: 635128488743542ff216a12cee14a03322549ce7 1698 1697 2007-08-15T16:46:00Z TobiasPaczian 17 /* SeedViewer */ wikitext text/x-wiki The SeedViewer, RAST-Server and MG-RAST-Server offer you a large number of statistics and detailed numbers about your organism. The purpose of this page is to explain how we calculate these numbers and what they mean. === MG-RAST === On the details page of your organism, you will find the following numbers: * ''Number of sequences'' : This is the total number of sequences submitted by the user for this genome. Not all of these will produce results later on. It is possible and very probable that some sequences can not be matched to anything in our database. * ''Total sequence length'' : This is the sum of the lengths of all submitted sequences. * ''Average read length'' : This is the '''Total sequence length''' divided by the '''Number of sequences''' * ''Longest sequence id' : This is the identifier string of the longest sequence submitted. * ''Longest sequence length'' : This is the length of the longest sequence submitted. * ''Shortest sequence id'' : This is the identifier string of the shortest sequence submitted. * ''Shortest sequence length'' : This is the length of the shortest sequence submitted === RAST === On the details page of your organism, you will find the following numbers: * ''Number of features'' : This is the number of features the RAST-Server could identify in your uploaded genome and match to our database. * ''Number of warnings'' : This is the number of warnings issued by the pipeline while processing your genome. This refers to inconsistencies detected, which are not fatal to annotation, but which should be investigated further. The numbers for each type of warnings are listed below. * ''Number of fatal problems'' : This is the number of problems which cause the pipeline to be unable to process your genome. These problems have to be addressed before the annotation process can finish. * ''Possibly missing genes'' : * ''Convergent overlaps'' : * ''Divergent overlaps'' : * ''Same strand overlaps'' : === SeedViewer === On the ''Organism Overview'' page, there are a number of statistical counts about the selected genome: * ''Size'' : This is the number of basepairs of sequence of this genome. * ''Number of Fragments'' : This is the number of fragments which included at least one coding sequence that could be matched to our database. * ''Number of Subsystems'' : * ''Number of Coding Sequences'' : * ''Number of RNAs'' : * ''Protein Encoding Genes'' : The numbers are given in absolute and percent value. They should add up to 100% (given rounding error) and their sum should be the equal to the number of coding sequences displayed on the left. : '''non-hypothetical''' : This is the number of coding sequences, which were annotated with a function which is not hypothetical. Values for hypothetical include a list of synonyms like ''hypothetical protein'' or ''putative protein'' : '''hypothetical''' : This is the number of coding sequences which were assigned to be hypothetical (or a synonym) 4005a5396db5ee8cac4ebd090003da465e4d6f9b 1699 1698 2007-08-15T16:48:41Z TobiasPaczian 17 /* SeedViewer */ wikitext text/x-wiki The SeedViewer, RAST-Server and MG-RAST-Server offer you a large number of statistics and detailed numbers about your organism. The purpose of this page is to explain how we calculate these numbers and what they mean. === MG-RAST === On the details page of your organism, you will find the following numbers: * ''Number of sequences'' : This is the total number of sequences submitted by the user for this genome. Not all of these will produce results later on. It is possible and very probable that some sequences can not be matched to anything in our database. * ''Total sequence length'' : This is the sum of the lengths of all submitted sequences. * ''Average read length'' : This is the '''Total sequence length''' divided by the '''Number of sequences''' * ''Longest sequence id' : This is the identifier string of the longest sequence submitted. * ''Longest sequence length'' : This is the length of the longest sequence submitted. * ''Shortest sequence id'' : This is the identifier string of the shortest sequence submitted. * ''Shortest sequence length'' : This is the length of the shortest sequence submitted === RAST === On the details page of your organism, you will find the following numbers: * ''Number of features'' : This is the number of features the RAST-Server could identify in your uploaded genome and match to our database. * ''Number of warnings'' : This is the number of warnings issued by the pipeline while processing your genome. This refers to inconsistencies detected, which are not fatal to annotation, but which should be investigated further. The numbers for each type of warnings are listed below. * ''Number of fatal problems'' : This is the number of problems which cause the pipeline to be unable to process your genome. These problems have to be addressed before the annotation process can finish. * ''Possibly missing genes'' : * ''Convergent overlaps'' : * ''Divergent overlaps'' : * ''Same strand overlaps'' : === SeedViewer === On the ''Organism Overview'' page, there are a number of statistical counts about the selected genome: * ''Size'' : This is the number of basepairs of sequence of this genome. * ''Number of Fragments'' : This is the number of fragments which included at least one coding sequence that could be matched to our database. * ''Number of Subsystems'' : The number of different subsystem in which at least one member was found in the fragments of the genome. * ''Number of Coding Sequences'' : The number of protein encoding genes found in the submitted fragments that matched against our database. * ''Number of RNAs'' : The number of RNAs found in the submitted fragments that matched against our database. * ''Protein Encoding Genes'' : The numbers are given in absolute and percent value. They should add up to 100% (given rounding error) and their sum should be the equal to the number of coding sequences displayed on the left. : '''non-hypothetical''' : This is the number of coding sequences, which were annotated with a function which is not hypothetical. Values for hypothetical include a list of synonyms like ''hypothetical protein'' or ''putative protein'' : '''hypothetical''' : This is the number of coding sequences which were assigned to be hypothetical (or a synonym) 609016c972ce0e4ebc0530e4c50872f156145361 1700 1699 2007-08-15T17:48:08Z TobiasPaczian 17 /* SeedViewer */ wikitext text/x-wiki The SeedViewer, RAST-Server and MG-RAST-Server offer you a large number of statistics and detailed numbers about your organism. The purpose of this page is to explain how we calculate these numbers and what they mean. === MG-RAST === On the details page of your organism, you will find the following numbers: * ''Number of sequences'' : This is the total number of sequences submitted by the user for this genome. Not all of these will produce results later on. It is possible and very probable that some sequences can not be matched to anything in our database. * ''Total sequence length'' : This is the sum of the lengths of all submitted sequences. * ''Average read length'' : This is the '''Total sequence length''' divided by the '''Number of sequences''' * ''Longest sequence id' : This is the identifier string of the longest sequence submitted. * ''Longest sequence length'' : This is the length of the longest sequence submitted. * ''Shortest sequence id'' : This is the identifier string of the shortest sequence submitted. * ''Shortest sequence length'' : This is the length of the shortest sequence submitted === RAST === On the details page of your organism, you will find the following numbers: * ''Number of features'' : This is the number of features the RAST-Server could identify in your uploaded genome and match to our database. * ''Number of warnings'' : This is the number of warnings issued by the pipeline while processing your genome. This refers to inconsistencies detected, which are not fatal to annotation, but which should be investigated further. The numbers for each type of warnings are listed below. * ''Number of fatal problems'' : This is the number of problems which cause the pipeline to be unable to process your genome. These problems have to be addressed before the annotation process can finish. * ''Possibly missing genes'' : * ''Convergent overlaps'' : * ''Divergent overlaps'' : * ''Same strand overlaps'' : === SeedViewer === On the ''Organism Overview'' page, there are a number of statistical counts about the selected genome: * ''Size'' : This is the number of basepairs of sequence of this genome. * ''Number of Fragments'' : This is the number of fragments which included at least one coding sequence that could be matched to our database. * ''Number of Subsystems'' : The number of different subsystem in which at least one member was found in the fragments of the genome. * ''Number of Coding Sequences'' : The number of protein encoding genes found in the submitted fragments that matched against our database. * ''Number of RNAs'' : The number of RNAs found in the submitted fragments that matched against our database. * ''Protein Encoding Genes'' : The numbers are given in absolute and percent value. They should add up to 100% (given rounding error) and their sum should be the equal to the number of coding sequences displayed on the left. : '''non-hypothetical''' : This is the number of coding sequences, which were annotated with a function which is not hypothetical. Values for hypothetical include a list of synonyms like ''hypothetical protein'' or ''putative protein'' : '''hypothetical''' : This is the number of coding sequences which were assigned to be hypothetical (or a synonym) * ''Subsystem Counts'' The numbers in the tree of the subsystem hierarchy represent the number of coding sequences which are part of the according group, subgroup, subsystem or role. Note that not every coding sequence is part of a subsystem and that a single CDS may be part of more than one subsytem. 3bf505024c5f301ea0b1cb9d3f4ca5eb30e8b2ea 0 1367 1701 1630 2007-08-15T22:03:21Z FolkerMeyer 2 /* SEED-Viewer */ wikitext text/x-wiki === Annotators SEED === The master copy for all data in the SEED environment. Users can not access this password protected site. All annotations are made available via the [[#SEED-Viewer| SEED-Viewer]] and the [[#Trial-SEED|Trial-SEED]]. === Annotation === please see [[#Assigning_a_gene_function_and_annotation| Assigning a gene function and annotation]] === Assigning a gene function and annotation === Annotators assign gene functions to genes, and we call this process annotation. In most contexts, people use the term annotation to refer to assignments of function to the genes within a single organism. We certainly use the term in this sense, but we also use it to describe the process of assigning functions to corresponding genes from numerous genomes. Our basic approach to annotation is to ask our annotators to annotate the genes included in a [[#subsystem|Subsystem]] (e.g., glycolysis) across all genomes. This process of annotation of the genes within a subsystem across a set of genomes, rather than annotation of genes within a single genome, allows our annotators to focus on a constrained set of functional roles and attempt to accurately identify exactly what variant, if any, of a subsystem exists in each of the genomes. We use the term annotation to refer to assigning functions to genes (either within a single organism or to a constrained set of gene/protein families across a set of organisms). This activity certainly is closely related to the construction of subsystems and protein families (which we call FIGfams), but we will describe those activities elsewhere. === Assignment === please see [[#Assigning_a_gene_function_and_annotation| Assigning a gene function and annotation]] === Bidirectional Best Hit (BBH) === The paper [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=EBI&pubmedid=10077608 The use of gene clusters to infer functional coupling] defines a Bidirectional Best Hit or BBH as follows: <blockquote> Given two genes Xa and Xb from two genomes Ga and Gb, Xa and Xb are called a “bidirectional best hit (BBH)” if and only if recognizable similarity exists between them (in our case, we required fasta3 scores lower than 1.0 × 10−5), there is no gene Zb in Gb that is more similar than Xb is to Xa, and there is no gene Za in Ga that is more similar than Xa is to Xb. Genes (Xa, Ya) from Ga and (Xb, Yb) from Gb form a “pair of close bidirectional best hits (PCBBH)” if and only if Xa and Ya are close, Xb and Yb are close, Xa and Xb are a BBH, and Ya and Yb are a BBH. </blockquote> === Clearinghouse === please see [[#SubsystemClearinghouse|Subsystem Clearinghouse]] ===Feature=== A feature is a defined region in the DNA. A PEG is the most prevalent feature type in the SEED. Some other feature types include RNA, prophage and pathogenicity islands. The format for a feature ID is fig|genome_id.feature_abbreviation.feature_number (ie fig|83333.1.peg.100 ). === FIGfam === FIGfams are protein families generated by the Fellowship for Interpretation of Genomes (FIG). These families are based on the collection of subsystems, as well as correspondences between genes in closely related strains (we describe the construction of FIGfams in a separate SOP). The important properties of these families are as follows: # Two PEGs which both occur within a single FIGfam are believed to have the same function. # There is a decision procedure associated with the family which can be invoked to determine whether or not a gene can be “safely” assigned the function associated with the family. === Functional role === The concept of functional role is both basic and primitive in the sense that we will not pretend to offer a precise definition. It corresponds roughly to a single logical role that a gene or gene product may play in the operation of a cell. === Gene function === The function of a protein-encoding gene (PEG) is the functional role played by the product of the gene or an expression describing a set of roles played by the encoded protein. The operators used to construct expressions and the meanings associated with the operators are described in http://www.nmpdr.org/FIG/Html/SEED_functions.html Genes other than PEGs can also be assigned functions (e.g., SSU rRNA). However, in most cases the functions assigned to genes other than PEGs tend not to be problematic. === Linking to the SEED === We support linking to the SEED using a generic mechanism: Base URL: http://www.theseed.org/linkin.cgi? {| |+ Supported SEED Identifiers for external use ! Entity type !! key !! identifier !! Example |- | Genome || genome || fig<nowiki>|</nowiki>83331.1 || [[http://www.theseed.org/linkin.cgi?genome=fig|83333.1 http://www.theseed.org/linkin.cgi?genome=fig&#124;83333.1]] |- | PEG || id || fig<nowiki>|</nowiki>83331.peg.123 || [[http://www.theseed.org/linkin.cgi?id=fig|83333.1.peg.123 http://www.theseed.org/linkin.cgi?id=fig&#124;83333.1.peg.123]] |- | RNA feature || id || fig<nowiki>|</nowiki>83331.rna.1 || [[http://www.theseed.org/linkin.cgi?id=fig|83333.1.rna.1 http://www.theseed.org/linkin.cgi?id=fig&#124;83333.1.rna.1]] |- |} SEED identifiers contain the NCBI taxonomy ID, thus if the taxonomy ID changes, we need to update our internal data accordingly. To provide stable external identifiers, we keep a list of IDs that have changed and display warning message informing the user of the change and provide a link to the new version of the data requested. === Metabolic Reconstruction === When we use the term metabolic reconstruction of a given genome we will simply mean the set of populated subsystems that contain the genome, the PEGs (and their assigned functions) that are connected to functional roles in these populated subsystems, and the specific variant code associated with the genome in each of the populated subsystems. === NMPDR pathogen genome === The NMPDR is responsible for five classes of genomes: # Campylobacter jejuni # Listeria monocytogenes # Staphylococcus aureus # Streptococcus pneumoniae and Streptococcus pyogenes # Pathogenic Vibrio === Pair of Close Homologs (PCH) === The paper [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=EBI&pubmedid=10077608 The use of gene clusters to infer functional coupling] defines a Pair of Close Homologs as follows: <blockquote> We can also define the concept of “pairs of close homologs” (PCHs) as follows: genes (X′a, Y′a) from Ga and (X′b, Y′b) from Gb form a PCH if and only if X′a and Y′a are close, X′b and Y′b are close, X′a and X′b are recognizably similar, and Y′a and Y′b are recognizably similar. Here, we will consider two genes to be recognizably similar if their gene products produce fasta3 scores lower than 1.0 × 10−5. We use a scoring scheme analogous to the one described for PCBBHs to evaluate the connections between PCHs, except that if Ga and Gb are the same genome, we assign an arbitrary “same-genome score” (“same-genome” pairs cannot occur for PCBBHs by definition, but for PCHs they are possible). Unlike PCBBHs from two very close genomes for which contiguity is completely uninformative in the vast majority of cases, PCHs allow recognition of gene clusters that play similar (but usually not identical) roles (such as two transport cassettes containing pairs of homologs) in the same or similar organisms. The arbitrary “same-genome score” should, we believe, have a value that is high enough to rank such instances as significant. </blockquote> === PEG === A Protein Encoding Gene (PEG) is equivalent to a CDS (Coding Sequence). === Populated Subsystem === please see [[#Subsystem|Subsystem]] === SEED-Viewer === The SEED Viewer is a web-based application that allows browsing of SEED data structures. We use the SEED-Viewer to provide a public read-only version of the SEED data with the latest data at: http://seed-viewer.theseed.org '''Please note''': The data is updated automatically every 24 hours. When citing or linking to the SEED please use this version. === Subsystem === A subsystem is a set of functional roles that an annotator has decided should be thought of as related. Frequently, subsystems represent the collection of [[#Functional_role|functional roles]] that make up a metabolic pathway, a complex (e.g., the ribosome), or a class of proteins (e.g., two-component signal-transduction proteins within Staphylococcus aureus). A '''populated subsystem''' is a subsystem with an attached spreadsheet. The rows of the spreadsheet represent genomes and the columns represent the functional roles of the spreadsheet. Each cell contains the identifiers of genes from the corresponding genome the implement the specific functional role. That is, a populated subsystem specifies which genes implement instances of the subsystem in each of the genomes. The rows of a populated genome are assigned '''variant codes''' which describe which of a set of possible variants of the subsystem exist within each genome (special codes expressing a total absence of the subsystem or remaining uncertainty exist). Construction of a large set of curated populated subsystems is at the center of the NMPDR and SEED annotation efforts. === Subsystem Clearing House === Since annotators can work on any machine (including the public SEED) the way to propagate subsystems is via http://clearinghouse.theseed.org/clearinghouse_browser.cgi? === Trial-SEED === A public, read-write copy of the SEED is made available on http://theseed.uchicago.edu/FIG/index.cgi '''Please note''': The data on this server is updated in irregular intervals. Users should not assume that annotations made on this system will persist. Please publish your annotations to the [[#Subsystem_clearing_house|Subsystem Clearing house]]. === Variant Code=== please see [[#Subsystem|Subsystem]] a9116fa747539ad078359bd82d51ef1242f7966d 1702 1701 2007-08-15T22:04:11Z FolkerMeyer 2 /* SEED-Viewer */ wikitext text/x-wiki === Annotators SEED === The master copy for all data in the SEED environment. Users can not access this password protected site. All annotations are made available via the [[#SEED-Viewer| SEED-Viewer]] and the [[#Trial-SEED|Trial-SEED]]. === Annotation === please see [[#Assigning_a_gene_function_and_annotation| Assigning a gene function and annotation]] === Assigning a gene function and annotation === Annotators assign gene functions to genes, and we call this process annotation. In most contexts, people use the term annotation to refer to assignments of function to the genes within a single organism. We certainly use the term in this sense, but we also use it to describe the process of assigning functions to corresponding genes from numerous genomes. Our basic approach to annotation is to ask our annotators to annotate the genes included in a [[#subsystem|Subsystem]] (e.g., glycolysis) across all genomes. This process of annotation of the genes within a subsystem across a set of genomes, rather than annotation of genes within a single genome, allows our annotators to focus on a constrained set of functional roles and attempt to accurately identify exactly what variant, if any, of a subsystem exists in each of the genomes. We use the term annotation to refer to assigning functions to genes (either within a single organism or to a constrained set of gene/protein families across a set of organisms). This activity certainly is closely related to the construction of subsystems and protein families (which we call FIGfams), but we will describe those activities elsewhere. === Assignment === please see [[#Assigning_a_gene_function_and_annotation| Assigning a gene function and annotation]] === Bidirectional Best Hit (BBH) === The paper [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=EBI&pubmedid=10077608 The use of gene clusters to infer functional coupling] defines a Bidirectional Best Hit or BBH as follows: <blockquote> Given two genes Xa and Xb from two genomes Ga and Gb, Xa and Xb are called a “bidirectional best hit (BBH)” if and only if recognizable similarity exists between them (in our case, we required fasta3 scores lower than 1.0 × 10−5), there is no gene Zb in Gb that is more similar than Xb is to Xa, and there is no gene Za in Ga that is more similar than Xa is to Xb. Genes (Xa, Ya) from Ga and (Xb, Yb) from Gb form a “pair of close bidirectional best hits (PCBBH)” if and only if Xa and Ya are close, Xb and Yb are close, Xa and Xb are a BBH, and Ya and Yb are a BBH. </blockquote> === Clearinghouse === please see [[#SubsystemClearinghouse|Subsystem Clearinghouse]] ===Feature=== A feature is a defined region in the DNA. A PEG is the most prevalent feature type in the SEED. Some other feature types include RNA, prophage and pathogenicity islands. The format for a feature ID is fig|genome_id.feature_abbreviation.feature_number (ie fig|83333.1.peg.100 ). === FIGfam === FIGfams are protein families generated by the Fellowship for Interpretation of Genomes (FIG). These families are based on the collection of subsystems, as well as correspondences between genes in closely related strains (we describe the construction of FIGfams in a separate SOP). The important properties of these families are as follows: # Two PEGs which both occur within a single FIGfam are believed to have the same function. # There is a decision procedure associated with the family which can be invoked to determine whether or not a gene can be “safely” assigned the function associated with the family. === Functional role === The concept of functional role is both basic and primitive in the sense that we will not pretend to offer a precise definition. It corresponds roughly to a single logical role that a gene or gene product may play in the operation of a cell. === Gene function === The function of a protein-encoding gene (PEG) is the functional role played by the product of the gene or an expression describing a set of roles played by the encoded protein. The operators used to construct expressions and the meanings associated with the operators are described in http://www.nmpdr.org/FIG/Html/SEED_functions.html Genes other than PEGs can also be assigned functions (e.g., SSU rRNA). However, in most cases the functions assigned to genes other than PEGs tend not to be problematic. === Linking to the SEED === We support linking to the SEED using a generic mechanism: Base URL: http://www.theseed.org/linkin.cgi? {| |+ Supported SEED Identifiers for external use ! Entity type !! key !! identifier !! Example |- | Genome || genome || fig<nowiki>|</nowiki>83331.1 || [[http://www.theseed.org/linkin.cgi?genome=fig|83333.1 http://www.theseed.org/linkin.cgi?genome=fig&#124;83333.1]] |- | PEG || id || fig<nowiki>|</nowiki>83331.peg.123 || [[http://www.theseed.org/linkin.cgi?id=fig|83333.1.peg.123 http://www.theseed.org/linkin.cgi?id=fig&#124;83333.1.peg.123]] |- | RNA feature || id || fig<nowiki>|</nowiki>83331.rna.1 || [[http://www.theseed.org/linkin.cgi?id=fig|83333.1.rna.1 http://www.theseed.org/linkin.cgi?id=fig&#124;83333.1.rna.1]] |- |} SEED identifiers contain the NCBI taxonomy ID, thus if the taxonomy ID changes, we need to update our internal data accordingly. To provide stable external identifiers, we keep a list of IDs that have changed and display warning message informing the user of the change and provide a link to the new version of the data requested. === Metabolic Reconstruction === When we use the term metabolic reconstruction of a given genome we will simply mean the set of populated subsystems that contain the genome, the PEGs (and their assigned functions) that are connected to functional roles in these populated subsystems, and the specific variant code associated with the genome in each of the populated subsystems. === NMPDR pathogen genome === The NMPDR is responsible for five classes of genomes: # Campylobacter jejuni # Listeria monocytogenes # Staphylococcus aureus # Streptococcus pneumoniae and Streptococcus pyogenes # Pathogenic Vibrio === Pair of Close Homologs (PCH) === The paper [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=EBI&pubmedid=10077608 The use of gene clusters to infer functional coupling] defines a Pair of Close Homologs as follows: <blockquote> We can also define the concept of “pairs of close homologs” (PCHs) as follows: genes (X′a, Y′a) from Ga and (X′b, Y′b) from Gb form a PCH if and only if X′a and Y′a are close, X′b and Y′b are close, X′a and X′b are recognizably similar, and Y′a and Y′b are recognizably similar. Here, we will consider two genes to be recognizably similar if their gene products produce fasta3 scores lower than 1.0 × 10−5. We use a scoring scheme analogous to the one described for PCBBHs to evaluate the connections between PCHs, except that if Ga and Gb are the same genome, we assign an arbitrary “same-genome score” (“same-genome” pairs cannot occur for PCBBHs by definition, but for PCHs they are possible). Unlike PCBBHs from two very close genomes for which contiguity is completely uninformative in the vast majority of cases, PCHs allow recognition of gene clusters that play similar (but usually not identical) roles (such as two transport cassettes containing pairs of homologs) in the same or similar organisms. The arbitrary “same-genome score” should, we believe, have a value that is high enough to rank such instances as significant. </blockquote> === PEG === A Protein Encoding Gene (PEG) is equivalent to a CDS (Coding Sequence). === Populated Subsystem === please see [[#Subsystem|Subsystem]] === SEED-Viewer === The SEED Viewer is a web-based application that allows browsing of SEED data structures. We use the SEED-Viewer to provide a public read-only version of the latest SEED data at: http://seed-viewer.theseed.org '''Please note''': The data is updated automatically every 24 hours. When citing or linking to the SEED please use this version. === Subsystem === A subsystem is a set of functional roles that an annotator has decided should be thought of as related. Frequently, subsystems represent the collection of [[#Functional_role|functional roles]] that make up a metabolic pathway, a complex (e.g., the ribosome), or a class of proteins (e.g., two-component signal-transduction proteins within Staphylococcus aureus). A '''populated subsystem''' is a subsystem with an attached spreadsheet. The rows of the spreadsheet represent genomes and the columns represent the functional roles of the spreadsheet. Each cell contains the identifiers of genes from the corresponding genome the implement the specific functional role. That is, a populated subsystem specifies which genes implement instances of the subsystem in each of the genomes. The rows of a populated genome are assigned '''variant codes''' which describe which of a set of possible variants of the subsystem exist within each genome (special codes expressing a total absence of the subsystem or remaining uncertainty exist). Construction of a large set of curated populated subsystems is at the center of the NMPDR and SEED annotation efforts. === Subsystem Clearing House === Since annotators can work on any machine (including the public SEED) the way to propagate subsystems is via http://clearinghouse.theseed.org/clearinghouse_browser.cgi? === Trial-SEED === A public, read-write copy of the SEED is made available on http://theseed.uchicago.edu/FIG/index.cgi '''Please note''': The data on this server is updated in irregular intervals. Users should not assume that annotations made on this system will persist. Please publish your annotations to the [[#Subsystem_clearing_house|Subsystem Clearing house]]. === Variant Code=== please see [[#Subsystem|Subsystem]] 3ac257ddedb70be7cb68848df777a10ac702cbee 0 1 1703 1666 2007-08-18T13:40:48Z FolkerMeyer 2 wikitext text/x-wiki With the growing number of available genomes, the need for an environment to support effective comparative analysis increases. The original SEED Project was started in 2003 by the [http://thefig.info Fellowship for Interpretation of Genomes (FIG)] as a largely unfunded open source effort. Argonne National Lab and the University of Chicago joined the project, and now much of the activity occurs at those two institutions (as well as the University of Illinois at Urbana-Champaign, Hope college, San Diego State University, the Burnham Institute and a number of other institutions). The cooperative effort focuses on the development of the comparative genomics environment called the SEED and, more importantly, on the development of curated genomic data. We provide a [http://seed-viewer.theseed.org/ SEED-Viewer] that allows read-only access to the latest curated data sets. For users interested in editing and learning how to use the system, we provide the [http://theseed.uchicago.edu/FIG/index.cgi Trial-SEED]. As described in our [[Annotating_1000_genomes|manifesto]] the [[Glossary#Annotation|annotation]] is not performed on a gene by gene basis per genome, but rather by [[Glossary#Subsystem|subsystem]] by an expert curator across many genomes at a time. Answering numerous requests for automatic Seed-Quality annotations for more or less complete bacterial and archaeal genomes, we have established the free [http://rast.nmpdr.org RAST-Server] (RAST=Rapid Annotation using Subsytems Technology). Using similar technology, we make the [http://metagenomics.nmpdr.org Metagenomics-RAST-Server] freely available. We make all our software and data available for download and use on our [[DownloadPage]] page. * When using the SEED, please cite: Overbeek et al., [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16214803&query_hl=2&itool=pubmed_docsum|Nucleic Acids Res 33(17)], 2005 ([http://www.theseed.org/SubsystemPaperSupplementalMaterial/index.html Supplementary material]) * Our approaches to annotation, gene calling etc are outlined in a series of [[SOPs|Standard Operating Procedures]]. 555c7899b18d99c09af6d10216ac2b0b93908523 1711 1703 2007-09-18T20:45:41Z WilliamMihalo 3 wikitext text/x-wiki With the growing number of available genomes, the need for an environment to support effective comparative analysis increases. The original SEED Project was started in 2003 by the [http://thefig.info Fellowship for Interpretation of Genomes (FIG)] as a largely unfunded open source effort. Argonne National Laboratory and the University of Chicago joined the project, and now much of the activity occurs at those two institutions (as well as the University of Illinois at Urbana-Champaign, Hope college, San Diego State University, the Burnham Institute and a number of other institutions). The cooperative effort focuses on the development of the comparative genomics environment called the SEED and, more importantly, on the development of curated genomic data. We provide a [http://seed-viewer.theseed.org/ SEED-Viewer] that allows read-only access to the latest curated data sets. For users interested in editing and learning how to use the system, we provide the [http://theseed.uchicago.edu/FIG/index.cgi Trial-SEED]. As described in our [[Annotating_1000_genomes|manifesto]] the [[Glossary#Annotation|annotation]] is not performed on a gene by gene basis per genome, but rather by [[Glossary#Subsystem|subsystem]] by an expert curator across many genomes at a time. Answering numerous requests for automatic Seed-Quality annotations for more or less complete bacterial and archaeal genomes, we have established the free [http://rast.nmpdr.org RAST-Server] (RAST=Rapid Annotation using Subsytems Technology). Using similar technology, we make the [http://metagenomics.nmpdr.org Metagenomics-RAST-Server] freely available. We make all our software and data available for download and use on our [[DownloadPage]] page. * When using the SEED, please cite: Overbeek et al., [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16214803&query_hl=2&itool=pubmed_docsum|Nucleic Acids Res 33(17)], 2005 ([http://www.theseed.org/SubsystemPaperSupplementalMaterial/index.html Supplementary material]) * Our approaches to annotation, gene calling etc are outlined in a series of [[SOPs|Standard Operating Procedures]]. 48da9be3248c039f2bf6e933953d8b778862c712 8 1090 1704 1667 2007-08-18T13:46:04Z FolkerMeyer 2 wikitext text/x-wiki * Navigation ** Home_of_the_SEED|Home of the SEED ** Annotating_1000_genomes|Manifesto ** SEED_People| SEED People ** Contact| Contact * SEEDs ** http://seed-viewer.theseed.org/|SEED-Viewer ** http://theseed.uchicago.edu/FIG/index.cgi|Trial-SEED * Applications ** http://rast.nmpdr.org/|RAST Annotation Server ** http://metagenomics.nmpdr.org/|Metagenomics RAST Server * Documentation ** RAST_Tutorial|RAST Server Tutorial ** SEED_Viewer_Tutorial|SEED Viewer Tutorial ** Video_Tutorials|Video Tutorials * Miscellaneous ** DownloadPage|Download Page ** Glossary|Glossary ** SOPs|SOPs ** SpecialPurposeDBs|Special Purpose DBs 36a63e06b9ca4967621a5c28c5a94a263aa57dcd 1706 1704 2007-08-24T15:42:15Z Marland 16 Addition of tutorial link for metagenomics RAST server. wikitext text/x-wiki * Navigation ** Home_of_the_SEED|Home of the SEED ** Annotating_1000_genomes|Manifesto ** SEED_People| SEED People ** Contact| Contact * SEEDs ** http://seed-viewer.theseed.org/|SEED-Viewer ** http://theseed.uchicago.edu/FIG/index.cgi|Trial-SEED * Applications ** http://rast.nmpdr.org/|RAST Annotation Server ** http://metagenomics.nmpdr.org/|Metagenomics RAST Server * Documentation ** RAST_Tutorial|RAST Server Tutorial ** MG_RAST_Tutorial||MG-RAST Tutorial ** SEED_Viewer_Tutorial|SEED Viewer Tutorial ** Video_Tutorials|Video Tutorials * Miscellaneous ** DownloadPage|Download Page ** Glossary|Glossary ** SOPs|SOPs ** SpecialPurposeDBs|Special Purpose DBs 08ca66b70513121b2395895409f9e51e0f0cfe37 1707 1706 2007-08-24T15:42:51Z Marland 16 removal of bar wikitext text/x-wiki * Navigation ** Home_of_the_SEED|Home of the SEED ** Annotating_1000_genomes|Manifesto ** SEED_People| SEED People ** Contact| Contact * SEEDs ** http://seed-viewer.theseed.org/|SEED-Viewer ** http://theseed.uchicago.edu/FIG/index.cgi|Trial-SEED * Applications ** http://rast.nmpdr.org/|RAST Annotation Server ** http://metagenomics.nmpdr.org/|Metagenomics RAST Server * Documentation ** RAST_Tutorial|RAST Server Tutorial ** MG_RAST_Tutorial|MG-RAST Tutorial ** SEED_Viewer_Tutorial|SEED Viewer Tutorial ** Video_Tutorials|Video Tutorials * Miscellaneous ** DownloadPage|Download Page ** Glossary|Glossary ** SOPs|SOPs ** SpecialPurposeDBs|Special Purpose DBs 0ac512be71af734b43484ef98c17488fd90ea8cc 0 1368 1705 1398 2007-08-18T13:47:52Z FolkerMeyer 2 wikitext text/x-wiki == This is the main SEED download page. == All tools and datasets that make up the SEED are in the public domain and can be downloaded at ftp://ftp.theseed.org 6d4a7986c4f42dc3e6d24c37463e6c300c7c8429 0 1433 1708 2007-08-24T18:08:28Z Marland 16 Addition of first portion of MG-RAST tutorial. wikitext text/x-wiki ===Overview=== The metagenomics RAST server (http://metagenomics.nmpdr.org) is a SEED-based environment that allows users to upload metagenomes for automated analyses. The server is built as a modified version of the RAST server. The RAST (Rapid Annotation using Subsystem Technology) technology was originally implemented to allow automated high-quality annotation of complete or draft microbial genomes using SEED data, and has been adapted for metagenome analysis. Our freely available server provides the annotation of sequence fragments, their phylogenetic classification, functional classification of samples, and comparison between multiple metagenomes. The server also computes an initial metabolic reconstruction for the metagenome and allows comparison of metabolic reconstructions of metagenomes and genomes. User submission and analysis are confidential. Although we do not guarantee a maximum turnover time, the current average processing time is about 24 hours. Currently the server handles 454 and Sanger sequence data. Data sets supplied by 454 can be uploaded directly. The server relies on the technology and data established by FIG and the NMPDR team at Argonne National Laboratory and the University of Chicago. In addition to SEED data we use the following ribosomal RNA databases for our analyses: GREENGENES, RDP-II and European ribosomal RNA database. ===Registration=== Registration is required for metagenome submission and viewing of results. This enables us to contact users once the computation is finished and in case the users intervention is required. At the bottom of the main page is a like for registration (see Figure 1). [[image:mg-rast-main-page.jpeg]] Required fields for registration include first and last name and your valid email address. Login information and other communication regarding the status of your metagenome analysis job(s) will be sent to the email address you provide. Optional information includes your organization and any notes you would like to send the rast server support team. Please note that your login and password are valid for use in both the MG-RAST and RAST servers. ===Submitting a Job=== Once you have registered and logged into the server, you will be directed to your Jobs Overview. At the top of this page will be a link labeled "Upload Genome" which will allow you to start a new job. Your metagenome file(s) should be uploaded as either a single plain text file containing all the sequences in FASTA format, or a gzip compressed tar archive (tar.gz) that has your FASTA sequences. Please do not upload uncompressed files larger than 30 MB. If your data set is larger, use the compressed format or contact us for other options. If you would like, you can also include the quality files in your archive. The fasta file names should end either *.fna, *.fa, or *.fasta, and the quality files should be named *.qual. The quality files are not currently used in the analysis, but the sequences will be renamed and renumbered along with the fasta sequences. If you have trouble with the upload format please email mg-rast@mcs.anl.gov and we'll be happy to help. ''Data entered into the server will not be used for any purposes or integrated into the main SEED environment, it will remain on this server for 120 days or until deleted by the submitting user.'' An email will be sent once the automatic annotation has finished or in case user intervention is required. ===Viewing Results=== The overall status of your metagenome analyses can be viewed from the main portion of the Jobs Overview page. This contains information regarding a user’s personal jobs and when applicable, jobs of the user’s organization. Information includes each job/metagenome and its status and contains information including job number, name of the user who started the job, metagenome name, and annotation progress. The table of jobs can be sorted on any column containing textual information. When the user has numerous metagenomes to select from, they can use the text boxes in the table header to search and refine the list of jobs. Clicking on the bars for a given job in the annotation progress column directs the user to the “Job Details” page where the detailed job status and access to the metagenome analysis can be found. 45c0d6bd4119580206fc560fa090f82cac24829c 6 1434 1709 2007-08-24T18:08:59Z Marland 16 wikitext text/x-wiki da39a3ee5e6b4b0d3255bfef95601890afd80709 0 1412 1710 1654 2007-08-24T18:15:45Z Marland 16 Added toc wikitext text/x-wiki ===The RAST Server Overview=== The RAST (Rapid Annotation using Subsystem Technology) Server provides high quality genome annotations for prokaryotes across the whole phylogenetic tree. It makes a SEED-quality annotation available as a service with a 48 hour turnaround time. The SEED environment and SEED data structures (most prominently FIGfams) are used to compute the automatic annotations; however data is not added into the SEED automatically. Once annotation is completed, genomes can be downloaded in a variety of formats or viewed online. The genome annotation provided does include a mapping of genes to subsystems and a metabolic reconstruction. Figure 1 provides an overview of the RAST Server and connections to the SEED Viewer. Getting Started: Registration is required for genome submission and viewing of results. This enables us to contact users once the computation is finished and in case the users intervention is required. [[Image:rast_fig1.jpg]] Figure 1. Overview of the RAST Server navigation, features and capabilities. ===Jobs Overview=== Upon logging onto the server, users are directed to the “Jobs Overview” page, which as the name suggests, provides a site for job management. Jobs Overview has two main components: starting a new job and reviewing submitted/completed jobs. Start a new job. The navigation bar (Figure 2) at the top of the page provides a pull down menu for job submission, logout, and review/edit user account information. To start a new job, users should select “Upload Genome” from the navigation bar or the link near the top of the page. The user is required to provide a valid taxonomy id+, the organism’s Genus, species, and strain, as well as a nucleotide sequence file in FASTA format. Optional parameters are suggested, but not required and include genetic code, sequencing method, coverage, number of contigs and average read length. Currently the server supports genome analysis of prokaryotes with genetic codes 4 and 11. ''+Taxonomy id’s can be obtained from the NCBI taxonomy browser (http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/). Search by organism name, and the taxonomy id is returned. For example, Escherichia coli K12 has taxonomy id 83333.'' [[Image:rast_fig2.jpg]] Figure 2. Jobs Overview Navigation Bar. ===Reviewing submitted/completed jobs=== The overall status of genome analysis can be viewed from the main portion of the Jobs Overview page. This contains information regarding a user’s personal jobs and when applicable, jobs of the user’s organization. Figure 3 shows an example account where the individual does not have any personal jobs, but has access to several for their organization. The table shows each job/genome and its status and contains information including job number, name of the user who started the job, genome id (taxonomy_id. internal_id), genome name, and annotation progress. The table of jobs can be sorted on any column containing textual information. When the user has numerous genomes to select from, they can use the text boxes in the table header to search and refine the list of jobs. Clicking on the bars for a given job in the annotation progress column directs the user to the “Job Details” page where the detailed job status and access to the genome analysis can be found. [[Image:rast_fig3.jpg]] Figure 3. Jobs Overview for a given account. ===Job Details=== For a given job, the Job Details page provides the user with information regarding the status of the genome annotation progress, as well as access to the results of the analysis upon completion. Account and job management links are found in the navigation bar at the top of the Job Details page (Figure 4) includes (1) logout, (2) upload a new genome, (3) link back to the Jobs Overview, and (4) review/edit your account information. [[Image:rast_fig4.jpg]] Figure 4. Job Details Navigation Bar. The Job Details page has three main functions: 1. To provide access to the results of the genome analysis via the SEED Viewer, 2. Export tool that enables the user to download the annotated genome in various formats (GTF, GenBank, GFF3, or EMBL) 3. The status of their genome analysis. Information regarding the status of each major step in the analysis process is reported which includes: * Genome upload ** Genome id and Name ** Job number ** Name of user who created the job ** Date and time of job submission * Rapid propagation (protein function annotation) * Quality check ** Statistics (number of features, warnings, fatal problems) ** Warnings (overlaps) ** Fatal Problems (embedded genes) * Quality revision (users approval) * Similarity Computation * Bidirectional Best Hit Computation (for conserved regions and functional coupling) * Auto Assignment (to subsystems) 7a90d86d920b9f624f737c7e751ceeba18db2f0c 0 1435 1712 2007-10-02T16:53:53Z DanielPaarmann 8 wikitext text/x-wiki === MG-RAST === On the details page of your organism, you will find the following numbers: * ''Number of sequences'' : This is the total number of sequences submitted by the user for this genome. Not all of these will produce results later on. It is possible and very probable that some sequences can not be matched to anything in our database. * ''Total sequence length'' : This is the sum of the lengths of all submitted sequences. * ''Average read length'' : This is the '''Total sequence length''' divided by the '''Number of sequences''' * ''Longest sequence id' : This is the identifier string of the longest sequence submitted. * ''Longest sequence length'' : This is the length of the longest sequence submitted. * ''Shortest sequence id'' : This is the identifier string of the shortest sequence submitted. * ''Shortest sequence length'' : This is the length of the shortest sequence submitted 1020b937569828b23313611806de7420d261e1da 1713 1712 2007-10-02T16:54:20Z DanielPaarmann 8 wikitext text/x-wiki === MG-RAST === On the details page of your organism, you will find the following numbers: * ''Number of sequences'' : This is the total number of sequences submitted by the user for this genome. Not all of these will produce results later on. It is possible and very probable that some sequences can not be matched to anything in our database. * ''Total sequence length'' : This is the sum of the lengths of all submitted sequences. * ''Average read length'' : This is the '''Total sequence length''' divided by the '''Number of sequences''' * ''Longest sequence id' : This is the identifier string of the longest sequence submitted. * ''Longest sequence length'' : This is the length of the longest sequence submitted. * ''Shortest sequence id'' : This is the identifier string of the shortest sequence submitted. * ''Shortest sequence length'' : This is the length of the shortest sequence submitted === SeedViewer === On the ''Organism Overview'' page, there are a number of statistical counts about the selected genome: * ''Size'' : This is the number of basepairs of sequence of this genome. * ''Number of Fragments'' : This is the number of fragments which included at least one coding sequence that could be matched to our database. * ''Number of Subsystems'' : The number of different subsystem in which at least one member was found in the fragments of the genome. * ''Number of Coding Sequences'' : The number of protein encoding genes found in the submitted fragments that matched against our database. * ''Number of RNAs'' : The number of RNAs found in the submitted fragments that matched against our database. * ''Protein Encoding Genes'' : The numbers are given in absolute and percent value. They should add up to 100% (given rounding error) and their sum should be the equal to the number of coding sequences displayed on the left. : '''non-hypothetical''' : This is the number of coding sequences, which were annotated with a function which is not hypothetical. Values for hypothetical include a list of synonyms like ''hypothetical protein'' or ''putative protein'' : '''hypothetical''' : This is the number of coding sequences which were assigned to be hypothetical (or a synonym) * ''Subsystem Counts'' The numbers in the tree of the subsystem hierarchy represent the number of coding sequences which are part of the according group, subgroup, subsystem or role. Note that not every coding sequence is part of a subsystem and that a single CDS may be part of more than one subsytem. c909a1a05af74fcd97a602feae85231a359a59b1 1714 1713 2007-10-02T16:55:07Z DanielPaarmann 8 wikitext text/x-wiki The MG-RAST-Server and SEED Viewer offer you a large number of statistics and detailed numbers about your organism. The purpose of this page is to explain how we calculate these numbers and what they mean. === MG-RAST === On the details page of your organism, you will find the following numbers: * ''Number of sequences'' : This is the total number of sequences submitted by the user for this genome. Not all of these will produce results later on. It is possible and very probable that some sequences can not be matched to anything in our database. * ''Total sequence length'' : This is the sum of the lengths of all submitted sequences. * ''Average read length'' : This is the '''Total sequence length''' divided by the '''Number of sequences''' * ''Longest sequence id' : This is the identifier string of the longest sequence submitted. * ''Longest sequence length'' : This is the length of the longest sequence submitted. * ''Shortest sequence id'' : This is the identifier string of the shortest sequence submitted. * ''Shortest sequence length'' : This is the length of the shortest sequence submitted === SeedViewer === On the ''Organism Overview'' page, there are a number of statistical counts about the selected genome: * ''Size'' : This is the number of basepairs of sequence of this genome. * ''Number of Fragments'' : This is the number of fragments which included at least one coding sequence that could be matched to our database. * ''Number of Subsystems'' : The number of different subsystem in which at least one member was found in the fragments of the genome. * ''Number of Coding Sequences'' : The number of protein encoding genes found in the submitted fragments that matched against our database. * ''Number of RNAs'' : The number of RNAs found in the submitted fragments that matched against our database. * ''Protein Encoding Genes'' : The numbers are given in absolute and percent value. They should add up to 100% (given rounding error) and their sum should be the equal to the number of coding sequences displayed on the left. : '''non-hypothetical''' : This is the number of coding sequences, which were annotated with a function which is not hypothetical. Values for hypothetical include a list of synonyms like ''hypothetical protein'' or ''putative protein'' : '''hypothetical''' : This is the number of coding sequences which were assigned to be hypothetical (or a synonym) * ''Subsystem Counts'' The numbers in the tree of the subsystem hierarchy represent the number of coding sequences which are part of the according group, subgroup, subsystem or role. Note that not every coding sequence is part of a subsystem and that a single CDS may be part of more than one subsytem. 54de3a72dbb82cb39612dd0799776db96441165e 1715 1714 2007-10-02T16:58:34Z DanielPaarmann 8 wikitext text/x-wiki The MG-RAST-Server and SEED Viewer offer you a large number of statistics and detailed numbers about your organism. The purpose of this page is to explain how we calculate these numbers and what they mean. === MG-RAST === On the details page of your organism, you will find the following numbers: * ''Number of sequences'' : This is the total number of sequences submitted by the user for this genome. Not all of these will produce results later on. It is possible and very probable that some sequences can not be matched to anything in our database. * ''Total sequence length'' : This is the sum of the lengths of all submitted sequences. * ''Average read length'' : This is the '''Total sequence length''' divided by the '''Number of sequences''' * ''Longest sequence id' : This is the identifier string of the longest sequence submitted. * ''Longest sequence length'' : This is the length of the longest sequence submitted. * ''Shortest sequence id'' : This is the identifier string of the shortest sequence submitted. * ''Shortest sequence length'' : This is the length of the shortest sequence submitted === SeedViewer === On the ''Metagenome Overview'' page, there are a number of statistical counts about the selected metagenome: * ''Size'' : This is the number of basepairs of sequence of this genome. '''Known bug:''' Unfortunately there is currently a bug which adds 1 to the length of each sequence. * ''Number of Fragments'' : This is the number of fragments which included at least one coding sequence that could be matched to our database. * ''Number of Subsystems'' : The number of different subsystem in which at least one member was found in the fragments of the genome. * ''Number of Coding Sequences'' : The number of protein encoding genes found in the submitted fragments that matched against our database. * ''Number of RNAs'' : The number of RNAs found in the submitted fragments that matched against our database. * ''Protein Encoding Genes'' : The numbers are given in absolute and percent value. They should add up to 100% (given rounding error) and their sum should be the equal to the number of coding sequences displayed on the left. : '''non-hypothetical''' : This is the number of coding sequences, which were annotated with a function which is not hypothetical. Values for hypothetical include a list of synonyms like ''hypothetical protein'' or ''putative protein'' : '''hypothetical''' : This is the number of coding sequences which were assigned to be hypothetical (or a synonym) * ''Subsystem Counts'' The numbers in the tree of the subsystem hierarchy represent the number of coding sequences which are part of the according group, subgroup, subsystem or role. Note that not every coding sequence is part of a subsystem and that a single CDS may be part of more than one subsytem. 4a50d661d30283384daee7aff1317d466a0a9c85 1716 1715 2007-10-02T16:59:08Z DanielPaarmann 8 wikitext text/x-wiki The MG-RAST-Server and SEED Viewer offer you a large number of statistics and detailed numbers about your organism. The purpose of this page is to explain how we calculate these numbers and what they mean. === MG-RAST === On the details page of your organism, you will find the following numbers: * ''Number of sequences'' : This is the total number of sequences submitted by the user for this genome. Not all of these will produce results later on. It is possible and very probable that some sequences can not be matched to anything in our database. * ''Total sequence length'' : This is the sum of the lengths of all submitted sequences. * ''Average read length'' : This is the '''Total sequence length''' divided by the '''Number of sequences''' * ''Longest sequence id' : This is the identifier string of the longest sequence submitted. * ''Longest sequence length'' : This is the length of the longest sequence submitted. * ''Shortest sequence id'' : This is the identifier string of the shortest sequence submitted. * ''Shortest sequence length'' : This is the length of the shortest sequence submitted === SeedViewer === On the ''Metagenome Overview'' page, there are a number of statistical counts about the selected metagenome: * ''Size'' : This is the number of basepairs of sequence of this genome. : '''Known bug:''' Unfortunately there is currently a bug which adds 1 to the length of each sequence. * ''Number of Fragments'' : This is the number of fragments which included at least one coding sequence that could be matched to our database. * ''Number of Subsystems'' : The number of different subsystem in which at least one member was found in the fragments of the genome. * ''Number of Coding Sequences'' : The number of protein encoding genes found in the submitted fragments that matched against our database. * ''Number of RNAs'' : The number of RNAs found in the submitted fragments that matched against our database. * ''Protein Encoding Genes'' : The numbers are given in absolute and percent value. They should add up to 100% (given rounding error) and their sum should be the equal to the number of coding sequences displayed on the left. : '''non-hypothetical''' : This is the number of coding sequences, which were annotated with a function which is not hypothetical. Values for hypothetical include a list of synonyms like ''hypothetical protein'' or ''putative protein'' : '''hypothetical''' : This is the number of coding sequences which were assigned to be hypothetical (or a synonym) * ''Subsystem Counts'' The numbers in the tree of the subsystem hierarchy represent the number of coding sequences which are part of the according group, subgroup, subsystem or role. Note that not every coding sequence is part of a subsystem and that a single CDS may be part of more than one subsytem. cfbe8709e11d3212dec8607b4bbd4c35c90066fa 1717 1716 2007-10-02T17:53:36Z DanielPaarmann 8 wikitext text/x-wiki The MG-RAST-Server and SEED Viewer offer you a large number of statistics and detailed numbers about your organism. The purpose of this page is to explain how we calculate these numbers and what they mean. === MG-RAST === On the details page of your organism, you will find the following numbers: * ''Number of sequences'' : This is the total number of sequences submitted by the user for this genome. Not all of these will produce results later on. It is possible and very probable that some sequences can not be matched to anything in our database. * ''Total sequence length'' : This is the sum of the lengths of all submitted sequences. * ''Average read length'' : This is the '''Total sequence length''' divided by the '''Number of sequences''' * ''Longest sequence id' : This is the identifier string of the longest sequence submitted. * ''Longest sequence length'' : This is the length of the longest sequence submitted. * ''Shortest sequence id'' : This is the identifier string of the shortest sequence submitted. * ''Shortest sequence length'' : This is the length of the shortest sequence submitted === SeedViewer === On the ''Metagenome Overview'' page, there are a number of statistical counts about the selected metagenome: * ''Size'' : This is the number of basepairs of sequence of this genome. : '''Known bug:''' Unfortunately there is currently a bug which shows a higher than actual sequence length. The MG-RAST Job Details page shows the correct sequence size. * ''Number of Fragments'' : This is the number of fragments which included at least one coding sequence that could be matched to our database. * ''Number of Subsystems'' : The number of different subsystem in which at least one member was found in the fragments of the genome. * ''Number of Coding Sequences'' : The number of protein encoding genes found in the submitted fragments that matched against our database. : '''Note:''' This number may be higher than the ''Number of Fragments'' if ... * ''Number of RNAs'' : The number of RNAs found in the submitted fragments that matched against our database. * ''Protein Encoding Genes'' : The numbers are given in absolute and percent value. They should add up to 100% (given rounding error) and their sum should be the equal to the number of coding sequences displayed on the left. : '''non-hypothetical''' : This is the number of coding sequences, which were annotated with a function which is not hypothetical. Values for hypothetical include a list of synonyms like ''hypothetical protein'' or ''putative protein'' : '''hypothetical''' : This is the number of coding sequences which were assigned to be hypothetical (or a synonym) * ''Subsystem Counts'' The numbers in the tree of the subsystem hierarchy represent the number of coding sequences which are part of the according group, subgroup, subsystem or role. Note that not every coding sequence is part of a subsystem and that a single CDS may be part of more than one subsytem. 37411ad6b8a6f55d9eae76135f3e8efc3e311cea 1718 1717 2007-10-02T21:36:16Z Marland 16 wikitext text/x-wiki The MG-RAST-Server and SEED Viewer offer you a large number of statistics and detailed numbers about your organism. The purpose of this page is to explain how we calculate these numbers and what they mean. === MG-RAST === On the details page of your organism, you will find the following numbers: * ''Number of sequences'' : This is the total number of sequences submitted by the user for this genome. Not all of these will produce results later on. It is possible and very probable that some sequences can not be matched to anything in our database. * ''Total sequence length'' : This is the sum of the lengths (bp) of all submitted sequences. * ''Average read length'' : This is the '''Total sequence length''' divided by the '''Number of sequences''' * ''Longest sequence id' : This is the identifier string of the longest sequence submitted. * ''Longest sequence length'' : This is the length (bp) of the longest sequence submitted. * ''Shortest sequence id'' : This is the identifier string of the shortest sequence submitted. * ''Shortest sequence length'' : This is the length of the shortest sequence submitted === SeedViewer === On the ''Metagenome Overview'' page, there are a number of statistical counts about the selected metagenome: * ''Size'' : This is the number of basepairs (total length) of all of the sequences submiited for a given metagenome. : '''Known bug:''' Unfortunately there is currently a bug which shows a higher than actual sequence length. The MG-RAST Job Details page shows the correct sequence size. * ''Number of Fragments'' : This is the number of submitted sequences which included at least one coding sequence that could be matched to our database. * ''Number of Subsystems'' : The number of different subsystems where one or more functional roles were found in the submitted fragments of the metagenome. * ''Number of Coding Sequences'' : The number of protein encoding genes found in the submitted fragments that matched against our database. : '''Note:''' This number may be higher than the ''Number of Fragments'' if ... * ''Number of RNAs'' : The number of RNAs found in the submitted fragments that matched against our database. * ''Protein Encoding Genes'' : The numbers are given in absolute and percent value. They should add up to 100% (given rounding error) and their sum should be the equal to the number of coding sequences displayed on the left. : '''non-hypothetical''' : This is the number of coding sequences, which were annotated with a function which is not hypothetical. Values for hypothetical include a list of synonyms like ''hypothetical protein'' or ''putative protein'' : '''hypothetical''' : This is the number of coding sequences which were assigned to be hypothetical (or a synonym) * ''Subsystem Counts'' The numbers in the tree of the subsystem hierarchy represent the number of coding sequences which are part of the according group, subgroup, subsystem or role. Note that not every coding sequence is part of a subsystem and that a single CDS may be part of more than one subsytem. === SeedViewer - Taxonomy === The taxnomic classification is calculated in several independent ways. First, all sequences are compared to the different rDNA databases: (1) RDP, (2)the European Ribosomal Database project, and (3)Greengenes. The criteria for a sequence being similar is a BLASTN E value < 1x10-5 and at least 50nt in the alignment. We also calculate the taxonomic profile of your sample from all the protein similarities computed to annotate the metagenome. The advantage of this approach is that we use a lot more data than is available for the 16S analysis, however, the disadvantage of this approach is that it is obviously limited to those genomes that are in our underlying SEED database. ed01030f54f08d81c8fdbccdc250052bb5105504 1719 1718 2007-10-03T15:17:04Z DanielPaarmann 8 wikitext text/x-wiki The MG-RAST-Server and SEED Viewer offer you a large number of statistics and detailed numbers about your metagenome. The purpose of this page is to explain how we calculate these numbers and what they mean. === MG-RAST === On the details page of your MG-Rast job, you will find the following numbers: * ''Number of sequences'' : This is the total number of sequences submitted by the user for this metagenome. Not all of these will produce results later on. It is possible and very probable that some sequences can not be matched to anything in our database. * ''Total sequence length'' : This is the sum of the lengths (bp) of all submitted sequences. * ''Average read length'' : This is the ''Total sequence length'' divided by the ''Number of sequences'' * ''Longest sequence id' : This is the identifier string of the longest sequence submitted. * ''Longest sequence length'' : This is the length (bp) of the longest sequence submitted. * ''Shortest sequence id'' : This is the identifier string of the shortest sequence submitted. * ''Shortest sequence length'' : This is the length of the shortest sequence submitted === SeedViewer === On the ''Metagenome Overview'' page, there are a number of statistical counts about the selected metagenome: * ''Size'' : This is the number of basepairs (total length) of all of the sequences submitted for a given metagenome. : '''Known bug:''' Unfortunately there is currently a bug which shows a higher than actual sequence length. The MG-RAST Job Details page shows the correct sequence size. * ''Number of Fragments'' : This is the number of submitted sequences which included at least one coding sequence that could be matched to our database. * ''Number of Subsystems'' : The number of different subsystems where one or more functional roles were found in the submitted fragments of the metagenome. * ''Number of Coding Sequences'' : The number of protein encoding genes found in the submitted fragments that matched against our database. : '''Note:''' This number may be higher than the ''Number of Fragments'' if there are multiple matches on a single fragment. * ''Number of RNAs'' : The number of RNAs found in the submitted fragments that matched against our database. * ''Protein Encoding Genes'' : The numbers are given in absolute and percent value. They should add up to 100% (given rounding error) and their sum should be the equal to the number of coding sequences displayed on the left. : '''non-hypothetical''' : This is the number of coding sequences, which were annotated with a function which is not hypothetical. Values for hypothetical include a list of synonyms like ''hypothetical protein'' or ''putative protein'' : '''hypothetical''' : This is the number of coding sequences which were assigned to be hypothetical (or a synonym) * ''Subsystem Counts'' The numbers in the tree of the subsystem hierarchy represent the number of coding sequences which are part of the according group, subgroup, subsystem or role. Note that not every coding sequence is part of a subsystem and that a single CDS may be part of more than one subsytem. === SeedViewer - Taxonomy === The taxonomic classification is calculated in several independent ways. First, all sequences are compared to the different rDNA databases: (1) RDP, (2)the European Ribosomal Database project, and (3)Greengenes. The criteria for a sequence being similar is a BLASTN E value < 1x10-5 and at least 50nt in the alignment. We also calculate the taxonomic profile of your sample from all the protein similarities computed to annotate the metagenome. The advantage of this approach is that we use a lot more data than is available for the 16S analysis, however, the disadvantage of this approach is that it is obviously limited to those genomes that are in our underlying SEED database. 6d183441644f4b3ce3ae468bb76d1ef1399c49d3 1720 1719 2007-10-03T15:17:23Z DanielPaarmann 8 wikitext text/x-wiki The MG-RAST-Server and SEED Viewer offer you a large number of statistics and detailed numbers about your metagenome. The purpose of this page is to explain how we calculate these numbers and what they mean. === MG-RAST === On the details page of your MG-Rast job, you will find the following numbers: * ''Number of sequences'' : This is the total number of sequences submitted by the user for this metagenome. Not all of these will produce results later on. It is possible and very probable that some sequences can not be matched to anything in our database. * ''Total sequence length'' : This is the sum of the lengths (bp) of all submitted sequences. * ''Average read length'' : This is the ''Total sequence length'' divided by the ''Number of sequences'' * ''Longest sequence id'' : This is the identifier string of the longest sequence submitted. * ''Longest sequence length'' : This is the length (bp) of the longest sequence submitted. * ''Shortest sequence id'' : This is the identifier string of the shortest sequence submitted. * ''Shortest sequence length'' : This is the length of the shortest sequence submitted === SeedViewer === On the ''Metagenome Overview'' page, there are a number of statistical counts about the selected metagenome: * ''Size'' : This is the number of basepairs (total length) of all of the sequences submitted for a given metagenome. : '''Known bug:''' Unfortunately there is currently a bug which shows a higher than actual sequence length. The MG-RAST Job Details page shows the correct sequence size. * ''Number of Fragments'' : This is the number of submitted sequences which included at least one coding sequence that could be matched to our database. * ''Number of Subsystems'' : The number of different subsystems where one or more functional roles were found in the submitted fragments of the metagenome. * ''Number of Coding Sequences'' : The number of protein encoding genes found in the submitted fragments that matched against our database. : '''Note:''' This number may be higher than the ''Number of Fragments'' if there are multiple matches on a single fragment. * ''Number of RNAs'' : The number of RNAs found in the submitted fragments that matched against our database. * ''Protein Encoding Genes'' : The numbers are given in absolute and percent value. They should add up to 100% (given rounding error) and their sum should be the equal to the number of coding sequences displayed on the left. : '''non-hypothetical''' : This is the number of coding sequences, which were annotated with a function which is not hypothetical. Values for hypothetical include a list of synonyms like ''hypothetical protein'' or ''putative protein'' : '''hypothetical''' : This is the number of coding sequences which were assigned to be hypothetical (or a synonym) * ''Subsystem Counts'' The numbers in the tree of the subsystem hierarchy represent the number of coding sequences which are part of the according group, subgroup, subsystem or role. Note that not every coding sequence is part of a subsystem and that a single CDS may be part of more than one subsytem. === SeedViewer - Taxonomy === The taxonomic classification is calculated in several independent ways. First, all sequences are compared to the different rDNA databases: (1) RDP, (2)the European Ribosomal Database project, and (3)Greengenes. The criteria for a sequence being similar is a BLASTN E value < 1x10-5 and at least 50nt in the alignment. We also calculate the taxonomic profile of your sample from all the protein similarities computed to annotate the metagenome. The advantage of this approach is that we use a lot more data than is available for the 16S analysis, however, the disadvantage of this approach is that it is obviously limited to those genomes that are in our underlying SEED database. 5139da262dadf4af09287daab27124f496c86ded 1721 1720 2007-10-03T15:54:18Z DanielPaarmann 8 wikitext text/x-wiki The MG-RAST-Server and SEED Viewer offer you a large number of statistics and detailed numbers about your metagenome. The purpose of this page is to explain how we calculate these numbers and what they mean. === MG-RAST === On the details page of your MG-Rast job, you will find the following numbers: * ''Number of sequences'' : This is the total number of sequences submitted by the user for this metagenome. Not all of these will produce results later on. It is possible and very probable that some sequences can not be matched to anything in our database. * ''Total sequence length'' : This is the sum of the lengths (bp) of all submitted sequences. * ''Average read length'' : This is the ''Total sequence length'' divided by the ''Number of sequences'' * ''Longest sequence id'' : This is the identifier string of the longest sequence submitted. * ''Longest sequence length'' : This is the length (bp) of the longest sequence submitted. * ''Shortest sequence id'' : This is the identifier string of the shortest sequence submitted. * ''Shortest sequence length'' : This is the length of the shortest sequence submitted === SeedViewer === On the ''Metagenome Overview'' page, there are a number of statistical counts about the selected metagenome: * ''Size'' : This is the number of basepairs (total length) of all of the sequences submitted for a given metagenome. : '''Known bug:''' Unfortunately there is currently a bug which shows a higher than actual sequence length. The MG-RAST Job Details page shows the correct sequence size. * ''Number of Fragments'' : This is the number of submitted sequences which included at least one coding sequence that could be matched to our database. * ''Number of Subsystems'' : The number of different subsystems where one or more functional roles were found in the submitted fragments of the metagenome. * ''Number of Coding Sequences'' : The number of protein encoding genes found in the submitted fragments that matched against our database. : '''Note:''' This number may be higher than the ''Number of Fragments'' if there are multiple matches on a single fragment. * ''Number of RNAs'' : The number of RNAs found in the submitted fragments that matched against our database. * ''Protein Encoding Genes'' : The numbers are given in absolute and percent value. They should add up to 100% (given rounding error) and their sum should be the equal to the number of coding sequences displayed on the left. : '''non-hypothetical''' : This is the number of coding sequences, which were annotated with a function which is not hypothetical. Values for hypothetical include a list of synonyms like ''hypothetical protein'' or ''putative protein'' : '''hypothetical''' : This is the number of coding sequences which were assigned to be hypothetical (or a synonym) * ''Subsystem Counts'' : The numbers in the tree of the subsystem hierarchy represent the number of coding sequences which are part of the according group, subgroup, subsystem or role. Note that not every coding sequence is part of a subsystem and that a single CDS may be part of more than one subsytem. === SeedViewer - Taxonomy === The taxonomic classification is calculated in several independent ways. First, all sequences are compared to the different rDNA databases: (1) RDP, (2)the European Ribosomal Database project, and (3)Greengenes. The criteria for a sequence being similar is a BLASTN E value < 1x10-5 and at least 50nt in the alignment. We also calculate the taxonomic profile of your sample from all the protein similarities computed to annotate the metagenome. The advantage of this approach is that we use a lot more data than is available for the 16S analysis, however, the disadvantage of this approach is that it is obviously limited to those genomes that are in our underlying SEED database. 80d3bdd164a20ea5a3796f6ae74f99776a4cbc22 0 1435 1722 1721 2007-10-03T15:55:53Z DanielPaarmann 8 /* SeedViewer */ wikitext text/x-wiki The MG-RAST-Server and SEED Viewer offer you a large number of statistics and detailed numbers about your metagenome. The purpose of this page is to explain how we calculate these numbers and what they mean. === MG-RAST === On the details page of your MG-Rast job, you will find the following numbers: * ''Number of sequences'' : This is the total number of sequences submitted by the user for this metagenome. Not all of these will produce results later on. It is possible and very probable that some sequences can not be matched to anything in our database. * ''Total sequence length'' : This is the sum of the lengths (bp) of all submitted sequences. * ''Average read length'' : This is the ''Total sequence length'' divided by the ''Number of sequences'' * ''Longest sequence id'' : This is the identifier string of the longest sequence submitted. * ''Longest sequence length'' : This is the length (bp) of the longest sequence submitted. * ''Shortest sequence id'' : This is the identifier string of the shortest sequence submitted. * ''Shortest sequence length'' : This is the length of the shortest sequence submitted === SeedViewer - Overview === On the ''Metagenome Overview'' page, there are a number of statistical counts about the selected metagenome: * ''Size'' : This is the number of basepairs (total length) of all of the sequences submitted for a given metagenome. : '''Known bug:''' Unfortunately there is currently a bug which shows a higher than actual sequence length. The MG-RAST Job Details page shows the correct sequence size. * ''Number of Fragments'' : This is the number of submitted sequences which included at least one coding sequence that could be matched to our database. * ''Number of Subsystems'' : The number of different subsystems where one or more functional roles were found in the submitted fragments of the metagenome. * ''Number of Coding Sequences'' : The number of protein encoding genes found in the submitted fragments that matched against our database. : '''Note:''' This number may be higher than the ''Number of Fragments'' if there are multiple matches on a single fragment. * ''Number of RNAs'' : The number of RNAs found in the submitted fragments that matched against our database. * ''Protein Encoding Genes'' : The numbers are given in absolute and percent value. They should add up to 100% (given rounding error) and their sum should be the equal to the number of coding sequences displayed on the left. : '''non-hypothetical''' : This is the number of coding sequences, which were annotated with a function which is not hypothetical. Values for hypothetical include a list of synonyms like ''hypothetical protein'' or ''putative protein'' : '''hypothetical''' : This is the number of coding sequences which were assigned to be hypothetical (or a synonym) * ''Subsystem Counts'' : The numbers in the tree of the subsystem hierarchy represent the number of coding sequences which are part of the according group, subgroup, subsystem or role. : '''Note:''' Not every coding sequence is part of a subsystem and a single coding sequence may fulfill functional roles in more than one subsystem (and thus be counted multiple times). === SeedViewer - Taxonomy === The taxonomic classification is calculated in several independent ways. First, all sequences are compared to the different rDNA databases: (1) RDP, (2)the European Ribosomal Database project, and (3)Greengenes. The criteria for a sequence being similar is a BLASTN E value < 1x10-5 and at least 50nt in the alignment. We also calculate the taxonomic profile of your sample from all the protein similarities computed to annotate the metagenome. The advantage of this approach is that we use a lot more data than is available for the 16S analysis, however, the disadvantage of this approach is that it is obviously limited to those genomes that are in our underlying SEED database. 6bba6844b905a9670f169ecaaf73b16f1cc011cd 1723 1722 2007-10-03T16:02:30Z DanielPaarmann 8 wikitext text/x-wiki The MG-RAST-Server and SEED Viewer offer you a large number of statistics and detailed numbers about your metagenome. The purpose of this page is to explain how we calculate these numbers and what they mean. === MG-RAST === On the details page of your MG-Rast job, you will find the following numbers: * ''Number of sequences'' : This is the total number of sequences submitted by the user for this metagenome. Not all of these will produce results later on. It is possible and very probable that some sequences can not be matched to anything in our database. * ''Total sequence length'' : This is the sum of the lengths (bp) of all submitted sequences. * ''Average read length'' : This is the ''Total sequence length'' divided by the ''Number of sequences'' * ''Longest sequence id'' : This is the identifier string of the longest sequence submitted. * ''Longest sequence length'' : This is the length (bp) of the longest sequence submitted. * ''Shortest sequence id'' : This is the identifier string of the shortest sequence submitted. * ''Shortest sequence length'' : This is the length of the shortest sequence submitted === SeedViewer - Overview === On the ''Metagenome Overview'' page, there are a number of statistical counts about the selected metagenome: * ''Size'' : This is the number of basepairs (total length) of all of the sequences submitted for a given metagenome. : '''Known bug:''' Unfortunately there is currently a bug which shows a higher than actual sequence length. The MG-RAST Job Details page shows the correct sequence size. * ''Number of Fragments'' : This is the number of submitted sequences which included at least one coding sequence that could be matched to our database. * ''Number of Subsystems'' : The number of different subsystems where one or more functional roles were found in the submitted fragments of the metagenome. * ''Number of Coding Sequences'' : The number of protein encoding genes found in the submitted fragments that matched against our database. : '''Note:''' This number may be higher than the ''Number of Fragments'' if there are multiple matches on a single fragment. * ''Number of RNAs'' : The number of RNAs found in the submitted fragments that matched against our database. * ''Protein Encoding Genes'' : The numbers are given in absolute and percent value. They should add up to 100% (given rounding error) : * ''non-hypothetical'' : This is the number of coding sequences, which were annotated with a function which is not hypothetical. Values for hypothetical include a list of synonyms like ''hypothetical protein'' or ''putative protein'' : * ''hypothetical'' : This is the number of coding sequences which were assigned to be hypothetical (or a synonym) : '''Known bug:''' In some cases coding sequences do not have any functional assignment, but are not counted as hypothetical protein. That causes hypothetical and non-hypothetical not to add up to the total number of fragments. * ''Subsystem Counts'' : The numbers in the tree of the subsystem hierarchy represent the number of coding sequences which are part of the according group, subgroup, subsystem or role. : '''Note:''' Not every coding sequence is part of a subsystem and a single coding sequence may fulfill functional roles in more than one subsystem (and thus be counted multiple times). === SeedViewer - Taxonomy === The taxonomic classification is calculated in several independent ways. First, all sequences are compared to the different rDNA databases: (1) RDP, (2)the European Ribosomal Database project, and (3)Greengenes. The criteria for a sequence being similar is a BLASTN E value < 1x10-5 and at least 50nt in the alignment. We also calculate the taxonomic profile of your sample from all the protein similarities computed to annotate the metagenome. The advantage of this approach is that we use a lot more data than is available for the 16S analysis, however, the disadvantage of this approach is that it is obviously limited to those genomes that are in our underlying SEED database. 4f17a1b0a710cbc1fccf1e13714b8adecf6dc7c7 1724 1723 2007-10-03T16:03:28Z DanielPaarmann 8 /* SeedViewer - Overview */ wikitext text/x-wiki The MG-RAST-Server and SEED Viewer offer you a large number of statistics and detailed numbers about your metagenome. The purpose of this page is to explain how we calculate these numbers and what they mean. === MG-RAST === On the details page of your MG-Rast job, you will find the following numbers: * ''Number of sequences'' : This is the total number of sequences submitted by the user for this metagenome. Not all of these will produce results later on. It is possible and very probable that some sequences can not be matched to anything in our database. * ''Total sequence length'' : This is the sum of the lengths (bp) of all submitted sequences. * ''Average read length'' : This is the ''Total sequence length'' divided by the ''Number of sequences'' * ''Longest sequence id'' : This is the identifier string of the longest sequence submitted. * ''Longest sequence length'' : This is the length (bp) of the longest sequence submitted. * ''Shortest sequence id'' : This is the identifier string of the shortest sequence submitted. * ''Shortest sequence length'' : This is the length of the shortest sequence submitted === SeedViewer - Overview === On the ''Metagenome Overview'' page, there are a number of statistical counts about the selected metagenome: * ''Size'' : This is the number of basepairs (total length) of all of the sequences submitted for a given metagenome. : '''Known bug:''' Unfortunately there is currently a bug which shows a higher than actual sequence length. The MG-RAST Job Details page shows the correct sequence size. * ''Number of Fragments'' : This is the number of submitted sequences which included at least one coding sequence that could be matched to our database. * ''Number of Subsystems'' : The number of different subsystems where one or more functional roles were found in the submitted fragments of the metagenome. * ''Number of Coding Sequences'' : The number of protein encoding genes found in the submitted fragments that matched against our database. : '''Note:''' This number may be higher than the ''Number of Fragments'' if there are multiple matches on a single fragment. * ''Number of RNAs'' : The number of RNAs found in the submitted fragments that matched against our database. * ''Protein Encoding Genes'' : The numbers are given in absolute and percent value. They should add up to 100% (given rounding error) : * ''non-hypothetical'' : This is the number of coding sequences, which were annotated with a function which is not hypothetical. Values for hypothetical include a list of synonyms like ''hypothetical protein'' or ''putative protein'' : * ''hypothetical'' : This is the number of coding sequences which were assigned to be hypothetical (or a synonym) : '''Known bug:''' In some cases coding sequences do not have any functional assignment, but are not counted as hypothetical protein. That causes the number of hypothetical and non-hypothetical coding sequences not to add up to the total number of fragments. * ''Subsystem Counts'' : The numbers in the tree of the subsystem hierarchy represent the number of coding sequences which are part of the according group, subgroup, subsystem or role. : '''Note:''' Not every coding sequence is part of a subsystem and a single coding sequence may fulfill functional roles in more than one subsystem (and thus be counted multiple times). === SeedViewer - Taxonomy === The taxonomic classification is calculated in several independent ways. First, all sequences are compared to the different rDNA databases: (1) RDP, (2)the European Ribosomal Database project, and (3)Greengenes. The criteria for a sequence being similar is a BLASTN E value < 1x10-5 and at least 50nt in the alignment. We also calculate the taxonomic profile of your sample from all the protein similarities computed to annotate the metagenome. The advantage of this approach is that we use a lot more data than is available for the 16S analysis, however, the disadvantage of this approach is that it is obviously limited to those genomes that are in our underlying SEED database. ce462ed5a858fa23bad12b261e34a4e3cc9b0415 1725 1724 2007-10-03T16:13:55Z DanielPaarmann 8 wikitext text/x-wiki The MG-RAST-Server and SEED Viewer offer you a large number of statistics and detailed numbers about your metagenome. The purpose of this page is to explain how we calculate these numbers and what they mean. === MG-RAST === On the details page of your MG-Rast job, you will find the following numbers: * ''Number of sequences'' : This is the total number of sequences submitted by the user for this metagenome. Not all of these will produce results later on. It is possible and very probable that some sequences can not be matched to anything in our database. * ''Total sequence length'' : This is the sum of the lengths (bp) of all submitted sequences. * ''Average read length'' : This is the ''Total sequence length'' divided by the ''Number of sequences'' * ''Longest sequence id'' : This is the identifier string of the longest sequence submitted. * ''Longest sequence length'' : This is the length (bp) of the longest sequence submitted. * ''Shortest sequence id'' : This is the identifier string of the shortest sequence submitted. * ''Shortest sequence length'' : This is the length of the shortest sequence submitted === SeedViewer - Overview === On the ''Metagenome Overview'' page, there are a number of statistical counts about the selected metagenome: * ''Size'' : This is the number of basepairs (total length) of all of the sequences submitted for a given metagenome. : '''Known bug:''' Unfortunately there is currently a bug which shows a higher than actual sequence length. The MG-RAST Job Details page shows the correct sequence size. * ''Number of Fragments'' : This is the number of submitted sequences which included at least one coding sequence that could be matched to our database. * ''Number of Subsystems'' : The number of different subsystems where one or more functional roles were found in the submitted fragments of the metagenome. * ''Number of Coding Sequences'' : The number of protein encoding genes found in the submitted fragments that matched against our database. : '''Note:''' This number may be higher than the ''Number of Fragments'' if there are multiple matches on a single fragment. * ''Number of RNAs'' : The number of RNAs found in the submitted fragments that matched against our database. * ''Protein Encoding Genes'' : The numbers are given in absolute and percent value. They should add up to 100% (given rounding error) : * ''non-hypothetical'' : This is the number of coding sequences, which were annotated with a function which is not hypothetical. Values for hypothetical include a list of synonyms like ''hypothetical protein'' or ''putative protein'' : * ''hypothetical'' : This is the number of coding sequences which were assigned to be hypothetical (or a synonym) : '''Known bug:''' In some cases coding sequences do not have any functional assignment, but are not counted as hypothetical protein. That causes the number of hypothetical and non-hypothetical coding sequences not to add up to the total number of fragments. * ''Subsystem Counts'' : The numbers in the tree of the subsystem hierarchy represent the number of coding sequences which are part of the according group, subgroup, subsystem or role. : '''Note:''' Not every coding sequence is part of a subsystem and a single coding sequence may fulfill functional roles in more than one subsystem (and thus be counted multiple times). === SeedViewer - Taxonomy === The taxonomic classification is calculated in several independent ways. First, all sequences are compared to the different rDNA databases: (1) RDP, (2)the European Ribosomal Database project, and (3)Greengenes. The criteria for a sequence being similar is a BLASTN E value < 1x10-5 and at least 50nt in the alignment. We also calculate the taxonomic profile of your sample from all the protein similarities computed to annotate the metagenome. The advantage of this approach is that we use a lot more data than is available for the 16S analysis, however, the disadvantage of this approach is that it is obviously limited to those genomes that are in our underlying SEED database. c0c65449e7830a468fee539c09cc522b6d65f39e 0 1433 1726 1708 2007-10-04T18:44:36Z RobEdwards 14 /* Overview */ wikitext text/x-wiki ===Overview=== The metagenomics RAST server (http://metagenomics.nmpdr.org) is a SEED-based environment that allows users to upload metagenomes for automated analyses. The server is built as a modified version of the RAST server. The RAST (Rapid Annotation using Subsystem Technology) technology was originally implemented to allow automated high-quality annotation of complete or draft microbial genomes using SEED data, and has been adapted for metagenome analysis. Our freely available server provides the annotation of sequence fragments, their phylogenetic classification, functional classification of samples, and comparison between multiple metagenomes. The server also computes an initial metabolic reconstruction for the metagenome and allows comparison of metabolic reconstructions of metagenomes and genomes. User submission and analysis are confidential. Although we do not guarantee a maximum turnover time, the current average processing time is about 24 hours. Currently the server handles 454 and Sanger sequence data. Data sets supplied by 454 can be uploaded directly. In either case, the data needs to be in [[Valid fasta format]] The server relies on the technology and data established by FIG and the NMPDR team at Argonne National Laboratory and the University of Chicago. In addition to SEED data we use the following ribosomal RNA databases for our analyses: GREENGENES, RDP-II and European ribosomal RNA database. ===Registration=== Registration is required for metagenome submission and viewing of results. This enables us to contact users once the computation is finished and in case the users intervention is required. At the bottom of the main page is a like for registration (see Figure 1). [[image:mg-rast-main-page.jpeg]] Required fields for registration include first and last name and your valid email address. Login information and other communication regarding the status of your metagenome analysis job(s) will be sent to the email address you provide. Optional information includes your organization and any notes you would like to send the rast server support team. Please note that your login and password are valid for use in both the MG-RAST and RAST servers. ===Submitting a Job=== Once you have registered and logged into the server, you will be directed to your Jobs Overview. At the top of this page will be a link labeled "Upload Genome" which will allow you to start a new job. Your metagenome file(s) should be uploaded as either a single plain text file containing all the sequences in FASTA format, or a gzip compressed tar archive (tar.gz) that has your FASTA sequences. Please do not upload uncompressed files larger than 30 MB. If your data set is larger, use the compressed format or contact us for other options. If you would like, you can also include the quality files in your archive. The fasta file names should end either *.fna, *.fa, or *.fasta, and the quality files should be named *.qual. The quality files are not currently used in the analysis, but the sequences will be renamed and renumbered along with the fasta sequences. If you have trouble with the upload format please email mg-rast@mcs.anl.gov and we'll be happy to help. ''Data entered into the server will not be used for any purposes or integrated into the main SEED environment, it will remain on this server for 120 days or until deleted by the submitting user.'' An email will be sent once the automatic annotation has finished or in case user intervention is required. ===Viewing Results=== The overall status of your metagenome analyses can be viewed from the main portion of the Jobs Overview page. This contains information regarding a user’s personal jobs and when applicable, jobs of the user’s organization. Information includes each job/metagenome and its status and contains information including job number, name of the user who started the job, metagenome name, and annotation progress. The table of jobs can be sorted on any column containing textual information. When the user has numerous metagenomes to select from, they can use the text boxes in the table header to search and refine the list of jobs. Clicking on the bars for a given job in the annotation progress column directs the user to the “Job Details” page where the detailed job status and access to the metagenome analysis can be found. f7d1391709736df44a4a0af8dd1be6f7c9b35326 1729 1726 2007-10-04T18:56:57Z RobEdwards 14 /* Overview */ wikitext text/x-wiki ===Overview=== The metagenomics RAST server (http://metagenomics.nmpdr.org) is a SEED-based environment that allows users to upload metagenomes for automated analyses. The server is built as a modified version of the RAST server. The RAST (Rapid Annotation using Subsystem Technology) technology was originally implemented to allow automated high-quality annotation of complete or draft microbial genomes using SEED data, and has been adapted for metagenome analysis. Our freely available server provides the annotation of sequence fragments, their phylogenetic classification, functional classification of samples, and comparison between multiple metagenomes. The server also computes an initial metabolic reconstruction for the metagenome and allows comparison of metabolic reconstructions of metagenomes and genomes. User submission and analysis are confidential. Although we do not guarantee a maximum turnover time, the current average processing time is about 24 hours. Currently the server handles 454 and Sanger sequence data. Data sets supplied by 454 can be uploaded directly. In either case, the data needs to be in [[Valid fasta format]]. For more information, please see [[Which Sequences Should I Upload, and Where]] The server relies on the technology and data established by FIG and the NMPDR team at Argonne National Laboratory and the University of Chicago. In addition to SEED data we use the following ribosomal RNA databases for our analyses: GREENGENES, RDP-II and European ribosomal RNA database. ===Registration=== Registration is required for metagenome submission and viewing of results. This enables us to contact users once the computation is finished and in case the users intervention is required. At the bottom of the main page is a like for registration (see Figure 1). [[image:mg-rast-main-page.jpeg]] Required fields for registration include first and last name and your valid email address. Login information and other communication regarding the status of your metagenome analysis job(s) will be sent to the email address you provide. Optional information includes your organization and any notes you would like to send the rast server support team. Please note that your login and password are valid for use in both the MG-RAST and RAST servers. ===Submitting a Job=== Once you have registered and logged into the server, you will be directed to your Jobs Overview. At the top of this page will be a link labeled "Upload Genome" which will allow you to start a new job. Your metagenome file(s) should be uploaded as either a single plain text file containing all the sequences in FASTA format, or a gzip compressed tar archive (tar.gz) that has your FASTA sequences. Please do not upload uncompressed files larger than 30 MB. If your data set is larger, use the compressed format or contact us for other options. If you would like, you can also include the quality files in your archive. The fasta file names should end either *.fna, *.fa, or *.fasta, and the quality files should be named *.qual. The quality files are not currently used in the analysis, but the sequences will be renamed and renumbered along with the fasta sequences. If you have trouble with the upload format please email mg-rast@mcs.anl.gov and we'll be happy to help. ''Data entered into the server will not be used for any purposes or integrated into the main SEED environment, it will remain on this server for 120 days or until deleted by the submitting user.'' An email will be sent once the automatic annotation has finished or in case user intervention is required. ===Viewing Results=== The overall status of your metagenome analyses can be viewed from the main portion of the Jobs Overview page. This contains information regarding a user’s personal jobs and when applicable, jobs of the user’s organization. Information includes each job/metagenome and its status and contains information including job number, name of the user who started the job, metagenome name, and annotation progress. The table of jobs can be sorted on any column containing textual information. When the user has numerous metagenomes to select from, they can use the text boxes in the table header to search and refine the list of jobs. Clicking on the bars for a given job in the annotation progress column directs the user to the “Job Details” page where the detailed job status and access to the metagenome analysis can be found. 457815be23cca80a946da2fd364ba2b1ab28906c 1733 1729 2007-10-05T07:26:20Z RobEdwards 14 /* Overview */ wikitext text/x-wiki ===Overview=== The metagenomics RAST server (http://metagenomics.nmpdr.org) is a SEED-based environment that allows users to upload metagenomes for automated analyses. The server is built as a modified version of the RAST server. The RAST (Rapid Annotation using Subsystem Technology) technology was originally implemented to allow automated high-quality annotation of complete or draft microbial genomes using SEED data, and has been adapted for metagenome analysis. Our freely available server provides the annotation of sequence fragments, their phylogenetic classification, functional classification of samples, and comparison between multiple metagenomes. The server also computes an initial metabolic reconstruction for the metagenome and allows comparison of metabolic reconstructions of metagenomes and genomes. User submission and analysis are confidential. Although we do not guarantee a maximum turnover time, the current average processing time is about 24 hours. Currently the server handles 454 and Sanger sequence data. Data sets supplied by 454 can be uploaded directly. In either case, the data needs to be in [[Valid fasta format]]. For more information, please see [[Which Sequences Should I Upload, and Where]]. For the metagenomics service please also read this explanation of [[sequence formats]]. The server relies on the technology and data established by FIG and the NMPDR team at Argonne National Laboratory and the University of Chicago. In addition to SEED data we use the following ribosomal RNA databases for our analyses: GREENGENES, RDP-II and European ribosomal RNA database. ===Registration=== Registration is required for metagenome submission and viewing of results. This enables us to contact users once the computation is finished and in case the users intervention is required. At the bottom of the main page is a like for registration (see Figure 1). [[image:mg-rast-main-page.jpeg]] Required fields for registration include first and last name and your valid email address. Login information and other communication regarding the status of your metagenome analysis job(s) will be sent to the email address you provide. Optional information includes your organization and any notes you would like to send the rast server support team. Please note that your login and password are valid for use in both the MG-RAST and RAST servers. ===Submitting a Job=== Once you have registered and logged into the server, you will be directed to your Jobs Overview. At the top of this page will be a link labeled "Upload Genome" which will allow you to start a new job. Your metagenome file(s) should be uploaded as either a single plain text file containing all the sequences in FASTA format, or a gzip compressed tar archive (tar.gz) that has your FASTA sequences. Please do not upload uncompressed files larger than 30 MB. If your data set is larger, use the compressed format or contact us for other options. If you would like, you can also include the quality files in your archive. The fasta file names should end either *.fna, *.fa, or *.fasta, and the quality files should be named *.qual. The quality files are not currently used in the analysis, but the sequences will be renamed and renumbered along with the fasta sequences. If you have trouble with the upload format please email mg-rast@mcs.anl.gov and we'll be happy to help. ''Data entered into the server will not be used for any purposes or integrated into the main SEED environment, it will remain on this server for 120 days or until deleted by the submitting user.'' An email will be sent once the automatic annotation has finished or in case user intervention is required. ===Viewing Results=== The overall status of your metagenome analyses can be viewed from the main portion of the Jobs Overview page. This contains information regarding a user’s personal jobs and when applicable, jobs of the user’s organization. Information includes each job/metagenome and its status and contains information including job number, name of the user who started the job, metagenome name, and annotation progress. The table of jobs can be sorted on any column containing textual information. When the user has numerous metagenomes to select from, they can use the text boxes in the table header to search and refine the list of jobs. Clicking on the bars for a given job in the annotation progress column directs the user to the “Job Details” page where the detailed job status and access to the metagenome analysis can be found. dc07640406141b1394c57e1fbc3bc3c7992813e7 1735 1733 2007-10-05T07:27:51Z RobEdwards 14 /* Overview */ wikitext text/x-wiki ===Overview=== The metagenomics RAST server (http://metagenomics.nmpdr.org) is a SEED-based environment that allows users to upload metagenomes for automated analyses. The server is built as a modified version of the RAST server. The RAST (Rapid Annotation using Subsystem Technology) technology was originally implemented to allow automated high-quality annotation of complete or draft microbial genomes using SEED data, and has been adapted for metagenome analysis. Our freely available server provides the annotation of sequence fragments, their phylogenetic classification, functional classification of samples, and comparison between multiple metagenomes. The server also computes an initial metabolic reconstruction for the metagenome and allows comparison of metabolic reconstructions of metagenomes and genomes. User submission and analysis are confidential. Although we do not guarantee a maximum turnover time, the current average processing time is about 24 hours. Currently the server handles 454 and Sanger sequence data. Data sets supplied by 454 can be uploaded directly. In either case, the data needs to be in [[Valid fasta format]]. For more information, please see [[Which Sequences Should I Upload, and Where]]. For the metagenomics service please also read this explanation of [[metagenomics sequence formats]]. The server relies on the technology and data established by FIG and the NMPDR team at Argonne National Laboratory and the University of Chicago. In addition to SEED data we use the following ribosomal RNA databases for our analyses: GREENGENES, RDP-II and European ribosomal RNA database. ===Registration=== Registration is required for metagenome submission and viewing of results. This enables us to contact users once the computation is finished and in case the users intervention is required. At the bottom of the main page is a like for registration (see Figure 1). [[image:mg-rast-main-page.jpeg]] Required fields for registration include first and last name and your valid email address. Login information and other communication regarding the status of your metagenome analysis job(s) will be sent to the email address you provide. Optional information includes your organization and any notes you would like to send the rast server support team. Please note that your login and password are valid for use in both the MG-RAST and RAST servers. ===Submitting a Job=== Once you have registered and logged into the server, you will be directed to your Jobs Overview. At the top of this page will be a link labeled "Upload Genome" which will allow you to start a new job. Your metagenome file(s) should be uploaded as either a single plain text file containing all the sequences in FASTA format, or a gzip compressed tar archive (tar.gz) that has your FASTA sequences. Please do not upload uncompressed files larger than 30 MB. If your data set is larger, use the compressed format or contact us for other options. If you would like, you can also include the quality files in your archive. The fasta file names should end either *.fna, *.fa, or *.fasta, and the quality files should be named *.qual. The quality files are not currently used in the analysis, but the sequences will be renamed and renumbered along with the fasta sequences. If you have trouble with the upload format please email mg-rast@mcs.anl.gov and we'll be happy to help. ''Data entered into the server will not be used for any purposes or integrated into the main SEED environment, it will remain on this server for 120 days or until deleted by the submitting user.'' An email will be sent once the automatic annotation has finished or in case user intervention is required. ===Viewing Results=== The overall status of your metagenome analyses can be viewed from the main portion of the Jobs Overview page. This contains information regarding a user’s personal jobs and when applicable, jobs of the user’s organization. Information includes each job/metagenome and its status and contains information including job number, name of the user who started the job, metagenome name, and annotation progress. The table of jobs can be sorted on any column containing textual information. When the user has numerous metagenomes to select from, they can use the text boxes in the table header to search and refine the list of jobs. Clicking on the bars for a given job in the annotation progress column directs the user to the “Job Details” page where the detailed job status and access to the metagenome analysis can be found. 52427860083a4a385d5c069c0237340f30e4ffba 1750 1735 2007-11-02T04:39:46Z RobEdwards 14 /* Overview */ wikitext text/x-wiki ===Overview=== The metagenomics RAST server (http://metagenomics.nmpdr.org) is a SEED-based environment that allows users to upload metagenomes for automated analyses. The server is built as a modified version of the RAST server. The RAST (Rapid Annotation using Subsystem Technology) technology was originally implemented to allow automated high-quality annotation of complete or draft microbial genomes using SEED data, and has been adapted for metagenome analysis. Our freely available server provides the annotation of sequence fragments, their phylogenetic classification, functional classification of samples, and comparison between multiple metagenomes. The server also computes an initial metabolic reconstruction for the metagenome and allows comparison of metabolic reconstructions of metagenomes and genomes. User submission and analysis are confidential. Although we do not guarantee a maximum turnover time, the current average processing time is about 24 hours. Currently the server handles 454 and Sanger sequence data. Data sets supplied by 454 can be uploaded directly. In either case, the data needs to be in [[Valid fasta format]]. For more information, please see [[Which Sequences Should I Upload, and Where]]. For the metagenomics service please also read this explanation of [[metagenomics sequence formats]]. The server relies on the technology and data established by FIG and the NMPDR team at Argonne National Laboratory and the University of Chicago. In addition to SEED data we use the following ribosomal RNA databases for our analyses: [http://greengenes.lbl.gov/cgi-bin/nph-index.cgi greengenes], [http://rdp.cme.msu.edu/ RDP-II] and [http://bioinformatics.psb.ugent.be/webtools/rRNA/ European ribosomal RNA database]. ===Registration=== Registration is required for metagenome submission and viewing of results. This enables us to contact users once the computation is finished and in case the users intervention is required. At the bottom of the main page is a like for registration (see Figure 1). [[image:mg-rast-main-page.jpeg]] Required fields for registration include first and last name and your valid email address. Login information and other communication regarding the status of your metagenome analysis job(s) will be sent to the email address you provide. Optional information includes your organization and any notes you would like to send the rast server support team. Please note that your login and password are valid for use in both the MG-RAST and RAST servers. ===Submitting a Job=== Once you have registered and logged into the server, you will be directed to your Jobs Overview. At the top of this page will be a link labeled "Upload Genome" which will allow you to start a new job. Your metagenome file(s) should be uploaded as either a single plain text file containing all the sequences in FASTA format, or a gzip compressed tar archive (tar.gz) that has your FASTA sequences. Please do not upload uncompressed files larger than 30 MB. If your data set is larger, use the compressed format or contact us for other options. If you would like, you can also include the quality files in your archive. The fasta file names should end either *.fna, *.fa, or *.fasta, and the quality files should be named *.qual. The quality files are not currently used in the analysis, but the sequences will be renamed and renumbered along with the fasta sequences. If you have trouble with the upload format please email mg-rast@mcs.anl.gov and we'll be happy to help. ''Data entered into the server will not be used for any purposes or integrated into the main SEED environment, it will remain on this server for 120 days or until deleted by the submitting user.'' An email will be sent once the automatic annotation has finished or in case user intervention is required. ===Viewing Results=== The overall status of your metagenome analyses can be viewed from the main portion of the Jobs Overview page. This contains information regarding a user’s personal jobs and when applicable, jobs of the user’s organization. Information includes each job/metagenome and its status and contains information including job number, name of the user who started the job, metagenome name, and annotation progress. The table of jobs can be sorted on any column containing textual information. When the user has numerous metagenomes to select from, they can use the text boxes in the table header to search and refine the list of jobs. Clicking on the bars for a given job in the annotation progress column directs the user to the “Job Details” page where the detailed job status and access to the metagenome analysis can be found. b664d09325fd6fc591d0661887e33970ec0533b0 1758 1750 2007-12-18T01:52:42Z Marland 16 wikitext text/x-wiki ===Overview=== The metagenomics RAST server (http://metagenomics.nmpdr.org) is a SEED-based environment that allows users to upload metagenomes for automated analyses. The server is built as a modified version of the RAST server. The RAST (Rapid Annotation using Subsystem Technology) technology was originally implemented to allow automated high-quality annotation of complete or draft microbial genomes using SEED data, and has been adapted for metagenome analysis. Our freely available server provides the annotation of sequence fragments, their phylogenetic classification, functional classification of samples, and comparison between multiple metagenomes. The server also computes an initial metabolic reconstruction for the metagenome and allows comparison of metabolic reconstructions of metagenomes and genomes. User submission and analysis are confidential. Although we do not guarantee a maximum turnover time, the current average processing time is about 24 hours. Currently the server handles 454 and Sanger sequence data. Data sets supplied by 454 can be uploaded directly. In either case, the data needs to be in [[Valid fasta format]]. For more information, please see [[Which Sequences Should I Upload, and Where]]. For the metagenomics service please also read this explanation of [[metagenomics sequence formats]]. The server relies on the technology and data established by FIG and the NMPDR team at Argonne National Laboratory and the University of Chicago. In addition to SEED data we use the following ribosomal RNA databases for our analyses: [http://greengenes.lbl.gov/cgi-bin/nph-index.cgi greengenes], [http://rdp.cme.msu.edu/ RDP-II] and [http://bioinformatics.psb.ugent.be/webtools/rRNA/ European ribosomal RNA database]. ===Registration=== Registration is required for metagenome submission and viewing of results. This enables us to contact users once the computation is finished and in case the users intervention is required. At the bottom of the main page is a like for registration (see Figure 1). [[image:mg-rast-main-page.jpeg]] Required fields for registration include first and last name and your valid email address. Login information and other communication regarding the status of your metagenome analysis job(s) will be sent to the email address you provide. Optional information includes your organization and any notes you would like to send the rast server support team. Please note that your login and password are valid for use in both the MG-RAST and RAST servers. ===Submitting a Job=== Once you have registered and logged into the server, you will be directed to your Jobs Overview. At the top of this page will be a link labeled "Upload Genome" which will allow you to start a new job. Your metagenome file(s) should be uploaded as either a single plain text file containing all the sequences in FASTA format, or a gzip compressed tar archive (tar.gz) that has your FASTA sequences. Please do not upload uncompressed files larger than 30 MB. If your data set is larger, use the compressed format or contact us for other options. If you would like, you can also include the quality files in your archive. The fasta file names should end either *.fna, *.fa, or *.fasta, and the quality files should be named *.qual. The quality files are not currently used in the analysis, but the sequences will be renamed and renumbered along with the fasta sequences. If you have trouble with the upload format please email mg-rast@mcs.anl.gov and we'll be happy to help. ''Data entered into the server will not be used for any purposes or integrated into the main SEED environment, it will remain on this server for 120 days or until deleted by the submitting user.'' An email will be sent once the automatic annotation has finished or in case user intervention is required. ===Viewing Results=== The overall status of your metagenome analyses can be viewed from the main portion of the Jobs Overview page. This contains information regarding a user’s personal jobs and when applicable, jobs of the user’s organization. Information includes each job/metagenome and its status and contains information including job number, name of the user who started the job, metagenome name, and annotation progress. The table of jobs can be sorted on any column containing textual information. When the user has numerous metagenomes to select from, they can use the text boxes in the table header to search and refine the list of jobs. Clicking on the bars for a given job in the annotation progress column directs the user to the “Job Details” page where the detailed job status and access to the metagenome analysis can be found ("Browse annotated genome in SEED Viewer"). Users can also download the results in compressed GenBank format. ===MetaGenome Overview=== The MetaGenome Overview provides the user with various statistics regarding their metagenome and details on how each of these numbers are calculated can be found at MG-RAST_Numbers. 4dcd36e1b9a63e9a3d5288112934900e00f62fcc 1759 1758 2007-12-18T02:20:35Z Marland 16 wikitext text/x-wiki ===Overview=== The metagenomics RAST server (http://metagenomics.nmpdr.org) is a SEED-based environment that allows users to upload metagenomes for automated analyses. The server is built as a modified version of the RAST server. The RAST (Rapid Annotation using Subsystem Technology) technology was originally implemented to allow automated high-quality annotation of complete or draft microbial genomes using SEED data, and has been adapted for metagenome analysis. Our freely available server provides the annotation of sequence fragments, their phylogenetic classification, functional classification of samples, and comparison between multiple metagenomes. The server also computes an initial metabolic reconstruction for the metagenome and allows comparison of metabolic reconstructions of metagenomes and genomes. User submission and analysis are confidential. Although we do not guarantee a maximum turnover time, the current average processing time is about 24 hours. Currently the server handles 454 and Sanger sequence data. Data sets supplied by 454 can be uploaded directly. In either case, the data needs to be in [[Valid fasta format]]. For more information, please see [[Which Sequences Should I Upload, and Where]]. For the metagenomics service please also read this explanation of [[metagenomics sequence formats]]. The server relies on the technology and data established by FIG and the NMPDR team at Argonne National Laboratory and the University of Chicago. In addition to SEED data we use the following ribosomal RNA databases for our analyses: [http://greengenes.lbl.gov/cgi-bin/nph-index.cgi greengenes], [http://rdp.cme.msu.edu/ RDP-II] and [http://bioinformatics.psb.ugent.be/webtools/rRNA/ European ribosomal RNA database]. ===Registration=== Registration is required for metagenome submission and viewing of results. This enables us to contact users once the computation is finished and in case the users intervention is required. At the bottom of the main page is a like for registration (see Figure 1). [[image:mg-rast-main-page.jpeg]] Required fields for registration include first and last name and your valid email address. Login information and other communication regarding the status of your metagenome analysis job(s) will be sent to the email address you provide. Optional information includes your organization and any notes you would like to send the rast server support team. Please note that your login and password are valid for use in both the MG-RAST and RAST servers. ===Submitting a Job=== Once you have registered and logged into the server, you will be directed to your Jobs Overview. At the top of this page will be a link labeled "Upload Genome" which will allow you to start a new job. Your metagenome file(s) should be uploaded as either a single plain text file containing all the sequences in FASTA format, or a gzip compressed tar archive (tar.gz) that has your FASTA sequences. Please do not upload uncompressed files larger than 30 MB. If your data set is larger, use the compressed format or contact us for other options. If you would like, you can also include the quality files in your archive. The fasta file names should end either *.fna, *.fa, or *.fasta, and the quality files should be named *.qual. The quality files are not currently used in the analysis, but the sequences will be renamed and renumbered along with the fasta sequences. If you have trouble with the upload format please email mg-rast@mcs.anl.gov and we'll be happy to help. ''Data entered into the server will not be used for any purposes or integrated into the main SEED environment, it will remain on this server for 120 days or until deleted by the submitting user.'' An email will be sent once the automatic annotation has finished or in case user intervention is required. ===Viewing Results=== The overall status of your metagenome analyses can be viewed from the main portion of the Jobs Overview page. This contains information regarding a user’s personal jobs and when applicable, jobs of the user’s organization. Information includes each job/metagenome and its status and contains information including job number, name of the user who started the job, metagenome name, and annotation progress. The table of jobs can be sorted on any column containing textual information. When the user has numerous metagenomes to select from, they can use the text boxes in the table header to search and refine the list of jobs. Clicking on the bars for a given job in the annotation progress column directs the user to the “Job Details” page where the detailed job status and access to the metagenome analysis can be found ("Browse annotated genome in SEED Viewer"). Users can also download the results in compressed GenBank format. ===MetaGenome Overview=== The MetaGenome Overview provides the user with various statistics regarding their metagenome and details on how each of these numbers are calculated can be found [[MG-RAST_Numbers|here]]. [[image:mg-rast-sample-overview.PNG|300px]] fddd79c40ef520e762522a870a043a72650dc351 1761 1759 2007-12-18T02:22:03Z Marland 16 wikitext text/x-wiki ===Overview=== The metagenomics RAST server (http://metagenomics.nmpdr.org) is a SEED-based environment that allows users to upload metagenomes for automated analyses. The server is built as a modified version of the RAST server. The RAST (Rapid Annotation using Subsystem Technology) technology was originally implemented to allow automated high-quality annotation of complete or draft microbial genomes using SEED data, and has been adapted for metagenome analysis. Our freely available server provides the annotation of sequence fragments, their phylogenetic classification, functional classification of samples, and comparison between multiple metagenomes. The server also computes an initial metabolic reconstruction for the metagenome and allows comparison of metabolic reconstructions of metagenomes and genomes. User submission and analysis are confidential. Although we do not guarantee a maximum turnover time, the current average processing time is about 24 hours. Currently the server handles 454 and Sanger sequence data. Data sets supplied by 454 can be uploaded directly. In either case, the data needs to be in [[Valid fasta format]]. For more information, please see [[Which Sequences Should I Upload, and Where]]. For the metagenomics service please also read this explanation of [[metagenomics sequence formats]]. The server relies on the technology and data established by FIG and the NMPDR team at Argonne National Laboratory and the University of Chicago. In addition to SEED data we use the following ribosomal RNA databases for our analyses: [http://greengenes.lbl.gov/cgi-bin/nph-index.cgi greengenes], [http://rdp.cme.msu.edu/ RDP-II] and [http://bioinformatics.psb.ugent.be/webtools/rRNA/ European ribosomal RNA database]. ===Registration=== Registration is required for metagenome submission and viewing of results. This enables us to contact users once the computation is finished and in case the users intervention is required. At the bottom of the main page is a like for registration (see Figure 1). [[image:mg-rast-main-page.jpeg]] Required fields for registration include first and last name and your valid email address. Login information and other communication regarding the status of your metagenome analysis job(s) will be sent to the email address you provide. Optional information includes your organization and any notes you would like to send the rast server support team. Please note that your login and password are valid for use in both the MG-RAST and RAST servers. ===Submitting a Job=== Once you have registered and logged into the server, you will be directed to your Jobs Overview. At the top of this page will be a link labeled "Upload Genome" which will allow you to start a new job. Your metagenome file(s) should be uploaded as either a single plain text file containing all the sequences in FASTA format, or a gzip compressed tar archive (tar.gz) that has your FASTA sequences. Please do not upload uncompressed files larger than 30 MB. If your data set is larger, use the compressed format or contact us for other options. If you would like, you can also include the quality files in your archive. The fasta file names should end either *.fna, *.fa, or *.fasta, and the quality files should be named *.qual. The quality files are not currently used in the analysis, but the sequences will be renamed and renumbered along with the fasta sequences. If you have trouble with the upload format please email mg-rast@mcs.anl.gov and we'll be happy to help. ''Data entered into the server will not be used for any purposes or integrated into the main SEED environment, it will remain on this server for 120 days or until deleted by the submitting user.'' An email will be sent once the automatic annotation has finished or in case user intervention is required. ===Viewing Results=== The overall status of your metagenome analyses can be viewed from the main portion of the Jobs Overview page. This contains information regarding a user’s personal jobs and when applicable, jobs of the user’s organization. Information includes each job/metagenome and its status and contains information including job number, name of the user who started the job, metagenome name, and annotation progress. The table of jobs can be sorted on any column containing textual information. When the user has numerous metagenomes to select from, they can use the text boxes in the table header to search and refine the list of jobs. Clicking on the bars for a given job in the annotation progress column directs the user to the “Job Details” page where the detailed job status and access to the metagenome analysis can be found ("Browse annotated genome in SEED Viewer"). Users can also download the results in compressed GenBank format. ===MetaGenome Overview=== The MetaGenome Overview provides the user with various statistics regarding their metagenome and details on how each of these numbers are calculated can be found [[MG-RAST_Numbers|here]]. [[image:mg-rast-sample-overview.PNG|300px]] 9c9aa293a4580224a55d6c9cea9870244325d18b 1762 1761 2007-12-18T02:23:36Z Marland 16 wikitext text/x-wiki ===Overview=== The metagenomics RAST server (http://metagenomics.nmpdr.org) is a SEED-based environment that allows users to upload metagenomes for automated analyses. The server is built as a modified version of the RAST server. The RAST (Rapid Annotation using Subsystem Technology) technology was originally implemented to allow automated high-quality annotation of complete or draft microbial genomes using SEED data, and has been adapted for metagenome analysis. Our freely available server provides the annotation of sequence fragments, their phylogenetic classification, functional classification of samples, and comparison between multiple metagenomes. The server also computes an initial metabolic reconstruction for the metagenome and allows comparison of metabolic reconstructions of metagenomes and genomes. User submission and analysis are confidential. Although we do not guarantee a maximum turnover time, the current average processing time is about 24 hours. Currently the server handles 454 and Sanger sequence data. Data sets supplied by 454 can be uploaded directly. In either case, the data needs to be in [[Valid fasta format]]. For more information, please see [[Which Sequences Should I Upload, and Where]]. For the metagenomics service please also read this explanation of [[metagenomics sequence formats]]. The server relies on the technology and data established by FIG and the NMPDR team at Argonne National Laboratory and the University of Chicago. In addition to SEED data we use the following ribosomal RNA databases for our analyses: [http://greengenes.lbl.gov/cgi-bin/nph-index.cgi greengenes], [http://rdp.cme.msu.edu/ RDP-II] and [http://bioinformatics.psb.ugent.be/webtools/rRNA/ European ribosomal RNA database]. ===Registration=== Registration is required for metagenome submission and viewing of results. This enables us to contact users once the computation is finished and in case the users intervention is required. At the bottom of the main page is a like for registration (see Figure 1). [[image:mg-rast-main-page.jpeg]] Required fields for registration include first and last name and your valid email address. Login information and other communication regarding the status of your metagenome analysis job(s) will be sent to the email address you provide. Optional information includes your organization and any notes you would like to send the rast server support team. Please note that your login and password are valid for use in both the MG-RAST and RAST servers. ===Submitting a Job=== Once you have registered and logged into the server, you will be directed to your Jobs Overview. At the top of this page will be a link labeled "Upload Genome" which will allow you to start a new job. Your metagenome file(s) should be uploaded as either a single plain text file containing all the sequences in FASTA format, or a gzip compressed tar archive (tar.gz) that has your FASTA sequences. Please do not upload uncompressed files larger than 30 MB. If your data set is larger, use the compressed format or contact us for other options. If you would like, you can also include the quality files in your archive. The fasta file names should end either *.fna, *.fa, or *.fasta, and the quality files should be named *.qual. The quality files are not currently used in the analysis, but the sequences will be renamed and renumbered along with the fasta sequences. If you have trouble with the upload format please email mg-rast@mcs.anl.gov and we'll be happy to help. ''Data entered into the server will not be used for any purposes or integrated into the main SEED environment, it will remain on this server for 120 days or until deleted by the submitting user.'' An email will be sent once the automatic annotation has finished or in case user intervention is required. ===Viewing Results=== The overall status of your metagenome analyses can be viewed from the main portion of the Jobs Overview page. This contains information regarding a user’s personal jobs and when applicable, jobs of the user’s organization. Information includes each job/metagenome and its status and contains information including job number, name of the user who started the job, metagenome name, and annotation progress. The table of jobs can be sorted on any column containing textual information. When the user has numerous metagenomes to select from, they can use the text boxes in the table header to search and refine the list of jobs. Clicking on the bars for a given job in the annotation progress column directs the user to the “Job Details” page where the detailed job status and access to the metagenome analysis can be found ("Browse annotated genome in SEED Viewer"). Users can also download the results in compressed GenBank format. ===MetaGenome Overview=== The MetaGenome Overview provides the user with various statistics regarding their metagenome and details on how each of these numbers are calculated can be found [[MG-RAST_Numbers|here]]. [[image:mg-rast-sample-overview.PNG|300px]] Users can search for a given function, subsystem or process in the table, or browse the Subsystem Overview. d0cbcc383f3e9876e15af91c4d2f1f97054fe5e9 1763 1762 2007-12-18T02:24:55Z Marland 16 wikitext text/x-wiki ===Overview=== The metagenomics RAST server (http://metagenomics.nmpdr.org) is a SEED-based environment that allows users to upload metagenomes for automated analyses. The server is built as a modified version of the RAST server. The RAST (Rapid Annotation using Subsystem Technology) technology was originally implemented to allow automated high-quality annotation of complete or draft microbial genomes using SEED data, and has been adapted for metagenome analysis. Our freely available server provides the annotation of sequence fragments, their phylogenetic classification, functional classification of samples, and comparison between multiple metagenomes. The server also computes an initial metabolic reconstruction for the metagenome and allows comparison of metabolic reconstructions of metagenomes and genomes. User submission and analysis are confidential. Although we do not guarantee a maximum turnover time, the current average processing time is about 24 hours. Currently the server handles 454 and Sanger sequence data. Data sets supplied by 454 can be uploaded directly. In either case, the data needs to be in [[Valid fasta format]]. For more information, please see [[Which Sequences Should I Upload, and Where]]. For the metagenomics service please also read this explanation of [[metagenomics sequence formats]]. The server relies on the technology and data established by FIG and the NMPDR team at Argonne National Laboratory and the University of Chicago. In addition to SEED data we use the following ribosomal RNA databases for our analyses: [http://greengenes.lbl.gov/cgi-bin/nph-index.cgi greengenes], [http://rdp.cme.msu.edu/ RDP-II] and [http://bioinformatics.psb.ugent.be/webtools/rRNA/ European ribosomal RNA database]. ===Registration=== Registration is required for metagenome submission and viewing of results. This enables us to contact users once the computation is finished and in case the users intervention is required. At the bottom of the main page is a like for registration (see Figure 1). [[image:mg-rast-main-page.jpeg]] Required fields for registration include first and last name and your valid email address. Login information and other communication regarding the status of your metagenome analysis job(s) will be sent to the email address you provide. Optional information includes your organization and any notes you would like to send the rast server support team. Please note that your login and password are valid for use in both the MG-RAST and RAST servers. ===Submitting a Job=== Once you have registered and logged into the server, you will be directed to your Jobs Overview. At the top of this page will be a link labeled "Upload Genome" which will allow you to start a new job. Your metagenome file(s) should be uploaded as either a single plain text file containing all the sequences in FASTA format, or a gzip compressed tar archive (tar.gz) that has your FASTA sequences. Please do not upload uncompressed files larger than 30 MB. If your data set is larger, use the compressed format or contact us for other options. If you would like, you can also include the quality files in your archive. The fasta file names should end either *.fna, *.fa, or *.fasta, and the quality files should be named *.qual. The quality files are not currently used in the analysis, but the sequences will be renamed and renumbered along with the fasta sequences. If you have trouble with the upload format please email mg-rast@mcs.anl.gov and we'll be happy to help. ''Data entered into the server will not be used for any purposes or integrated into the main SEED environment, it will remain on this server for 120 days or until deleted by the submitting user.'' An email will be sent once the automatic annotation has finished or in case user intervention is required. ===Viewing Results=== The overall status of your metagenome analyses can be viewed from the main portion of the Jobs Overview page. This contains information regarding a user’s personal jobs and when applicable, jobs of the user’s organization. Information includes each job/metagenome and its status and contains information including job number, name of the user who started the job, metagenome name, and annotation progress. The table of jobs can be sorted on any column containing textual information. When the user has numerous metagenomes to select from, they can use the text boxes in the table header to search and refine the list of jobs. Clicking on the bars for a given job in the annotation progress column directs the user to the “Job Details” page where the detailed job status and access to the metagenome analysis can be found ("Browse annotated genome in SEED Viewer"). Users can also download the results in compressed GenBank format. ===MetaGenome Overview=== The MetaGenome Overview provides the user with various statistics regarding their metagenome and details on how each of these numbers are calculated can be found [[MG-RAST_Numbers|here]]. [[Image:mg-rast-sample-overview.png|300px]] [[Image:create_problem_set.png|300px]] Users can search for a given function, subsystem or process in the table, or browse the Subsystem Overview. f4a8d7c302c4697e6f3a208336373655df0897da 1765 1763 2007-12-18T02:25:45Z Marland 16 /* MetaGenome Overview */ wikitext text/x-wiki ===Overview=== The metagenomics RAST server (http://metagenomics.nmpdr.org) is a SEED-based environment that allows users to upload metagenomes for automated analyses. The server is built as a modified version of the RAST server. The RAST (Rapid Annotation using Subsystem Technology) technology was originally implemented to allow automated high-quality annotation of complete or draft microbial genomes using SEED data, and has been adapted for metagenome analysis. Our freely available server provides the annotation of sequence fragments, their phylogenetic classification, functional classification of samples, and comparison between multiple metagenomes. The server also computes an initial metabolic reconstruction for the metagenome and allows comparison of metabolic reconstructions of metagenomes and genomes. User submission and analysis are confidential. Although we do not guarantee a maximum turnover time, the current average processing time is about 24 hours. Currently the server handles 454 and Sanger sequence data. Data sets supplied by 454 can be uploaded directly. In either case, the data needs to be in [[Valid fasta format]]. For more information, please see [[Which Sequences Should I Upload, and Where]]. For the metagenomics service please also read this explanation of [[metagenomics sequence formats]]. The server relies on the technology and data established by FIG and the NMPDR team at Argonne National Laboratory and the University of Chicago. In addition to SEED data we use the following ribosomal RNA databases for our analyses: [http://greengenes.lbl.gov/cgi-bin/nph-index.cgi greengenes], [http://rdp.cme.msu.edu/ RDP-II] and [http://bioinformatics.psb.ugent.be/webtools/rRNA/ European ribosomal RNA database]. ===Registration=== Registration is required for metagenome submission and viewing of results. This enables us to contact users once the computation is finished and in case the users intervention is required. At the bottom of the main page is a like for registration (see Figure 1). [[image:mg-rast-main-page.jpeg]] Required fields for registration include first and last name and your valid email address. Login information and other communication regarding the status of your metagenome analysis job(s) will be sent to the email address you provide. Optional information includes your organization and any notes you would like to send the rast server support team. Please note that your login and password are valid for use in both the MG-RAST and RAST servers. ===Submitting a Job=== Once you have registered and logged into the server, you will be directed to your Jobs Overview. At the top of this page will be a link labeled "Upload Genome" which will allow you to start a new job. Your metagenome file(s) should be uploaded as either a single plain text file containing all the sequences in FASTA format, or a gzip compressed tar archive (tar.gz) that has your FASTA sequences. Please do not upload uncompressed files larger than 30 MB. If your data set is larger, use the compressed format or contact us for other options. If you would like, you can also include the quality files in your archive. The fasta file names should end either *.fna, *.fa, or *.fasta, and the quality files should be named *.qual. The quality files are not currently used in the analysis, but the sequences will be renamed and renumbered along with the fasta sequences. If you have trouble with the upload format please email mg-rast@mcs.anl.gov and we'll be happy to help. ''Data entered into the server will not be used for any purposes or integrated into the main SEED environment, it will remain on this server for 120 days or until deleted by the submitting user.'' An email will be sent once the automatic annotation has finished or in case user intervention is required. ===Viewing Results=== The overall status of your metagenome analyses can be viewed from the main portion of the Jobs Overview page. This contains information regarding a user’s personal jobs and when applicable, jobs of the user’s organization. Information includes each job/metagenome and its status and contains information including job number, name of the user who started the job, metagenome name, and annotation progress. The table of jobs can be sorted on any column containing textual information. When the user has numerous metagenomes to select from, they can use the text boxes in the table header to search and refine the list of jobs. Clicking on the bars for a given job in the annotation progress column directs the user to the “Job Details” page where the detailed job status and access to the metagenome analysis can be found ("Browse annotated genome in SEED Viewer"). Users can also download the results in compressed GenBank format. ===MetaGenome Overview=== The MetaGenome Overview provides the user with various statistics regarding their metagenome and details on how each of these numbers are calculated can be found [[MG-RAST_Numbers|here]]. [[Image:Mg-rast-sample-overview.png|300px]] Users can search for a given function, subsystem or process in the table, or browse the Subsystem Overview. b9186c7425a310ced562a7d1b9b0ac36d5d7c302 1766 1765 2007-12-18T02:26:25Z Marland 16 wikitext text/x-wiki ===Overview=== The metagenomics RAST server (http://metagenomics.nmpdr.org) is a SEED-based environment that allows users to upload metagenomes for automated analyses. The server is built as a modified version of the RAST server. The RAST (Rapid Annotation using Subsystem Technology) technology was originally implemented to allow automated high-quality annotation of complete or draft microbial genomes using SEED data, and has been adapted for metagenome analysis. Our freely available server provides the annotation of sequence fragments, their phylogenetic classification, functional classification of samples, and comparison between multiple metagenomes. The server also computes an initial metabolic reconstruction for the metagenome and allows comparison of metabolic reconstructions of metagenomes and genomes. User submission and analysis are confidential. Although we do not guarantee a maximum turnover time, the current average processing time is about 24 hours. Currently the server handles 454 and Sanger sequence data. Data sets supplied by 454 can be uploaded directly. In either case, the data needs to be in [[Valid fasta format]]. For more information, please see [[Which Sequences Should I Upload, and Where]]. For the metagenomics service please also read this explanation of [[metagenomics sequence formats]]. The server relies on the technology and data established by FIG and the NMPDR team at Argonne National Laboratory and the University of Chicago. In addition to SEED data we use the following ribosomal RNA databases for our analyses: [http://greengenes.lbl.gov/cgi-bin/nph-index.cgi greengenes], [http://rdp.cme.msu.edu/ RDP-II] and [http://bioinformatics.psb.ugent.be/webtools/rRNA/ European ribosomal RNA database]. ===Registration=== Registration is required for metagenome submission and viewing of results. This enables us to contact users once the computation is finished and in case the users intervention is required. At the bottom of the main page is a like for registration (see Figure 1). [[image:mg-rast-main-page.jpeg]] Required fields for registration include first and last name and your valid email address. Login information and other communication regarding the status of your metagenome analysis job(s) will be sent to the email address you provide. Optional information includes your organization and any notes you would like to send the rast server support team. Please note that your login and password are valid for use in both the MG-RAST and RAST servers. ===Submitting a Job=== Once you have registered and logged into the server, you will be directed to your Jobs Overview. At the top of this page will be a link labeled "Upload Genome" which will allow you to start a new job. Your metagenome file(s) should be uploaded as either a single plain text file containing all the sequences in FASTA format, or a gzip compressed tar archive (tar.gz) that has your FASTA sequences. Please do not upload uncompressed files larger than 30 MB. If your data set is larger, use the compressed format or contact us for other options. If you would like, you can also include the quality files in your archive. The fasta file names should end either *.fna, *.fa, or *.fasta, and the quality files should be named *.qual. The quality files are not currently used in the analysis, but the sequences will be renamed and renumbered along with the fasta sequences. If you have trouble with the upload format please email mg-rast@mcs.anl.gov and we'll be happy to help. ''Data entered into the server will not be used for any purposes or integrated into the main SEED environment, it will remain on this server for 120 days or until deleted by the submitting user.'' An email will be sent once the automatic annotation has finished or in case user intervention is required. ===Viewing Results=== The overall status of your metagenome analyses can be viewed from the main portion of the Jobs Overview page. This contains information regarding a user’s personal jobs and when applicable, jobs of the user’s organization. Information includes each job/metagenome and its status and contains information including job number, name of the user who started the job, metagenome name, and annotation progress. The table of jobs can be sorted on any column containing textual information. When the user has numerous metagenomes to select from, they can use the text boxes in the table header to search and refine the list of jobs. Clicking on the bars for a given job in the annotation progress column directs the user to the “Job Details” page where the detailed job status and access to the metagenome analysis can be found ("Browse annotated genome in SEED Viewer"). Users can also download the results in compressed GenBank format. ===MetaGenome Overview=== The MetaGenome Overview provides the user with various statistics regarding their metagenome and details on how each of these numbers are calculated can be found [[MG-RAST_Numbers|here]]. [[Image:mg-rast-sample-overview.png]] Users can search for a given function, subsystem or process in the table, or browse the Subsystem Overview. 862b36e4f36d6d16bb05b36506327ca2aa560946 1768 1766 2007-12-18T02:28:42Z Marland 16 /* MetaGenome Overview */ wikitext text/x-wiki ===Overview=== The metagenomics RAST server (http://metagenomics.nmpdr.org) is a SEED-based environment that allows users to upload metagenomes for automated analyses. The server is built as a modified version of the RAST server. The RAST (Rapid Annotation using Subsystem Technology) technology was originally implemented to allow automated high-quality annotation of complete or draft microbial genomes using SEED data, and has been adapted for metagenome analysis. Our freely available server provides the annotation of sequence fragments, their phylogenetic classification, functional classification of samples, and comparison between multiple metagenomes. The server also computes an initial metabolic reconstruction for the metagenome and allows comparison of metabolic reconstructions of metagenomes and genomes. User submission and analysis are confidential. Although we do not guarantee a maximum turnover time, the current average processing time is about 24 hours. Currently the server handles 454 and Sanger sequence data. Data sets supplied by 454 can be uploaded directly. In either case, the data needs to be in [[Valid fasta format]]. For more information, please see [[Which Sequences Should I Upload, and Where]]. For the metagenomics service please also read this explanation of [[metagenomics sequence formats]]. The server relies on the technology and data established by FIG and the NMPDR team at Argonne National Laboratory and the University of Chicago. In addition to SEED data we use the following ribosomal RNA databases for our analyses: [http://greengenes.lbl.gov/cgi-bin/nph-index.cgi greengenes], [http://rdp.cme.msu.edu/ RDP-II] and [http://bioinformatics.psb.ugent.be/webtools/rRNA/ European ribosomal RNA database]. ===Registration=== Registration is required for metagenome submission and viewing of results. This enables us to contact users once the computation is finished and in case the users intervention is required. At the bottom of the main page is a like for registration (see Figure 1). [[image:mg-rast-main-page.jpeg]] Required fields for registration include first and last name and your valid email address. Login information and other communication regarding the status of your metagenome analysis job(s) will be sent to the email address you provide. Optional information includes your organization and any notes you would like to send the rast server support team. Please note that your login and password are valid for use in both the MG-RAST and RAST servers. ===Submitting a Job=== Once you have registered and logged into the server, you will be directed to your Jobs Overview. At the top of this page will be a link labeled "Upload Genome" which will allow you to start a new job. Your metagenome file(s) should be uploaded as either a single plain text file containing all the sequences in FASTA format, or a gzip compressed tar archive (tar.gz) that has your FASTA sequences. Please do not upload uncompressed files larger than 30 MB. If your data set is larger, use the compressed format or contact us for other options. If you would like, you can also include the quality files in your archive. The fasta file names should end either *.fna, *.fa, or *.fasta, and the quality files should be named *.qual. The quality files are not currently used in the analysis, but the sequences will be renamed and renumbered along with the fasta sequences. If you have trouble with the upload format please email mg-rast@mcs.anl.gov and we'll be happy to help. ''Data entered into the server will not be used for any purposes or integrated into the main SEED environment, it will remain on this server for 120 days or until deleted by the submitting user.'' An email will be sent once the automatic annotation has finished or in case user intervention is required. ===Viewing Results=== The overall status of your metagenome analyses can be viewed from the main portion of the Jobs Overview page. This contains information regarding a user’s personal jobs and when applicable, jobs of the user’s organization. Information includes each job/metagenome and its status and contains information including job number, name of the user who started the job, metagenome name, and annotation progress. The table of jobs can be sorted on any column containing textual information. When the user has numerous metagenomes to select from, they can use the text boxes in the table header to search and refine the list of jobs. Clicking on the bars for a given job in the annotation progress column directs the user to the “Job Details” page where the detailed job status and access to the metagenome analysis can be found ("Browse annotated genome in SEED Viewer"). Users can also download the results in compressed GenBank format. ===MetaGenome Overview=== The MetaGenome Overview provides the user with various statistics regarding their metagenome and details on how each of these numbers are calculated can be found [[MG-RAST_Numbers|here]]. [[Image:MG-RAST-sample-overview.png]] Users can search for a given function, subsystem or process in the table, or browse the Subsystem Overview. 9b665f29a6a4e3e7c9a7fed1910c28d10b2a10d6 1770 1768 2007-12-18T02:29:43Z Marland 16 /* Registration */ wikitext text/x-wiki ===Overview=== The metagenomics RAST server (http://metagenomics.nmpdr.org) is a SEED-based environment that allows users to upload metagenomes for automated analyses. The server is built as a modified version of the RAST server. The RAST (Rapid Annotation using Subsystem Technology) technology was originally implemented to allow automated high-quality annotation of complete or draft microbial genomes using SEED data, and has been adapted for metagenome analysis. Our freely available server provides the annotation of sequence fragments, their phylogenetic classification, functional classification of samples, and comparison between multiple metagenomes. The server also computes an initial metabolic reconstruction for the metagenome and allows comparison of metabolic reconstructions of metagenomes and genomes. User submission and analysis are confidential. Although we do not guarantee a maximum turnover time, the current average processing time is about 24 hours. Currently the server handles 454 and Sanger sequence data. Data sets supplied by 454 can be uploaded directly. In either case, the data needs to be in [[Valid fasta format]]. For more information, please see [[Which Sequences Should I Upload, and Where]]. For the metagenomics service please also read this explanation of [[metagenomics sequence formats]]. The server relies on the technology and data established by FIG and the NMPDR team at Argonne National Laboratory and the University of Chicago. In addition to SEED data we use the following ribosomal RNA databases for our analyses: [http://greengenes.lbl.gov/cgi-bin/nph-index.cgi greengenes], [http://rdp.cme.msu.edu/ RDP-II] and [http://bioinformatics.psb.ugent.be/webtools/rRNA/ European ribosomal RNA database]. ===Registration=== Registration is required for metagenome submission and viewing of results. This enables us to contact users once the computation is finished and in case the users intervention is required. At the bottom of the main page is a like for registration (see Figure 1). [[Image:mg-rast-main-page.jpeg]] Required fields for registration include first and last name and your valid email address. Login information and other communication regarding the status of your metagenome analysis job(s) will be sent to the email address you provide. Optional information includes your organization and any notes you would like to send the rast server support team. Please note that your login and password are valid for use in both the MG-RAST and RAST servers. ===Submitting a Job=== Once you have registered and logged into the server, you will be directed to your Jobs Overview. At the top of this page will be a link labeled "Upload Genome" which will allow you to start a new job. Your metagenome file(s) should be uploaded as either a single plain text file containing all the sequences in FASTA format, or a gzip compressed tar archive (tar.gz) that has your FASTA sequences. Please do not upload uncompressed files larger than 30 MB. If your data set is larger, use the compressed format or contact us for other options. If you would like, you can also include the quality files in your archive. The fasta file names should end either *.fna, *.fa, or *.fasta, and the quality files should be named *.qual. The quality files are not currently used in the analysis, but the sequences will be renamed and renumbered along with the fasta sequences. If you have trouble with the upload format please email mg-rast@mcs.anl.gov and we'll be happy to help. ''Data entered into the server will not be used for any purposes or integrated into the main SEED environment, it will remain on this server for 120 days or until deleted by the submitting user.'' An email will be sent once the automatic annotation has finished or in case user intervention is required. ===Viewing Results=== The overall status of your metagenome analyses can be viewed from the main portion of the Jobs Overview page. This contains information regarding a user’s personal jobs and when applicable, jobs of the user’s organization. Information includes each job/metagenome and its status and contains information including job number, name of the user who started the job, metagenome name, and annotation progress. The table of jobs can be sorted on any column containing textual information. When the user has numerous metagenomes to select from, they can use the text boxes in the table header to search and refine the list of jobs. Clicking on the bars for a given job in the annotation progress column directs the user to the “Job Details” page where the detailed job status and access to the metagenome analysis can be found ("Browse annotated genome in SEED Viewer"). Users can also download the results in compressed GenBank format. ===MetaGenome Overview=== The MetaGenome Overview provides the user with various statistics regarding their metagenome and details on how each of these numbers are calculated can be found [[MG-RAST_Numbers|here]]. [[Image:MG-RAST-sample-overview.png]] Users can search for a given function, subsystem or process in the table, or browse the Subsystem Overview. 44e477b05860357b1d0eb1e7bf2725b416b807e7 1771 1770 2007-12-18T03:02:57Z Marland 16 /* MetaGenome Overview */ wikitext text/x-wiki ===Overview=== The metagenomics RAST server (http://metagenomics.nmpdr.org) is a SEED-based environment that allows users to upload metagenomes for automated analyses. The server is built as a modified version of the RAST server. The RAST (Rapid Annotation using Subsystem Technology) technology was originally implemented to allow automated high-quality annotation of complete or draft microbial genomes using SEED data, and has been adapted for metagenome analysis. Our freely available server provides the annotation of sequence fragments, their phylogenetic classification, functional classification of samples, and comparison between multiple metagenomes. The server also computes an initial metabolic reconstruction for the metagenome and allows comparison of metabolic reconstructions of metagenomes and genomes. User submission and analysis are confidential. Although we do not guarantee a maximum turnover time, the current average processing time is about 24 hours. Currently the server handles 454 and Sanger sequence data. Data sets supplied by 454 can be uploaded directly. In either case, the data needs to be in [[Valid fasta format]]. For more information, please see [[Which Sequences Should I Upload, and Where]]. For the metagenomics service please also read this explanation of [[metagenomics sequence formats]]. The server relies on the technology and data established by FIG and the NMPDR team at Argonne National Laboratory and the University of Chicago. In addition to SEED data we use the following ribosomal RNA databases for our analyses: [http://greengenes.lbl.gov/cgi-bin/nph-index.cgi greengenes], [http://rdp.cme.msu.edu/ RDP-II] and [http://bioinformatics.psb.ugent.be/webtools/rRNA/ European ribosomal RNA database]. ===Registration=== Registration is required for metagenome submission and viewing of results. This enables us to contact users once the computation is finished and in case the users intervention is required. At the bottom of the main page is a like for registration (see Figure 1). [[Image:mg-rast-main-page.jpeg]] Required fields for registration include first and last name and your valid email address. Login information and other communication regarding the status of your metagenome analysis job(s) will be sent to the email address you provide. Optional information includes your organization and any notes you would like to send the rast server support team. Please note that your login and password are valid for use in both the MG-RAST and RAST servers. ===Submitting a Job=== Once you have registered and logged into the server, you will be directed to your Jobs Overview. At the top of this page will be a link labeled "Upload Genome" which will allow you to start a new job. Your metagenome file(s) should be uploaded as either a single plain text file containing all the sequences in FASTA format, or a gzip compressed tar archive (tar.gz) that has your FASTA sequences. Please do not upload uncompressed files larger than 30 MB. If your data set is larger, use the compressed format or contact us for other options. If you would like, you can also include the quality files in your archive. The fasta file names should end either *.fna, *.fa, or *.fasta, and the quality files should be named *.qual. The quality files are not currently used in the analysis, but the sequences will be renamed and renumbered along with the fasta sequences. If you have trouble with the upload format please email mg-rast@mcs.anl.gov and we'll be happy to help. ''Data entered into the server will not be used for any purposes or integrated into the main SEED environment, it will remain on this server for 120 days or until deleted by the submitting user.'' An email will be sent once the automatic annotation has finished or in case user intervention is required. ===Viewing Results=== The overall status of your metagenome analyses can be viewed from the main portion of the Jobs Overview page. This contains information regarding a user’s personal jobs and when applicable, jobs of the user’s organization. Information includes each job/metagenome and its status and contains information including job number, name of the user who started the job, metagenome name, and annotation progress. The table of jobs can be sorted on any column containing textual information. When the user has numerous metagenomes to select from, they can use the text boxes in the table header to search and refine the list of jobs. Clicking on the bars for a given job in the annotation progress column directs the user to the “Job Details” page where the detailed job status and access to the metagenome analysis can be found ("Browse annotated genome in SEED Viewer"). Users can also download the results in compressed GenBank format. ===MetaGenome Overview=== The MetaGenome Overview provides the user with various statistics regarding their metagenome and details on how each of these numbers are calculated can be found [[MG-RAST_Numbers|here]]. [[Image:MG-RAST-sample-overview.png]] Users can search for a given function, subsystem or process in the table, or browse the Subsystem Overview. At the top right hand side of the page is a set of tabs that offer a wide set of information to browse, explore, compare and download. Browse allows users to look through the features of this metagenome either graphically or through a table. Both allow quick navigation and filtering for features of your interest. Each feature is linked to its own detail page. Explore allows users to view scenarios. Scenarios are isolated metabolic divisions that in aggregate represent the metabolic functionality of the metagenome. Each scenario is tested for reaction availability against the annotated functions. They provide the foundation for generating a metabolic reconstruction. Comparison of two metagenomes is also possible via the compare tab. You can also export all information about this metagenome (e.g. annotations, scenarios, subsystems) into a variety of formats (e.g. EMBL, Excel) for further analysis on your own system. c6a3a9972fe9ef9f30e9a94c24bab528dce4decf 0 1436 1727 2007-10-04T18:53:58Z RobEdwards 14 wikitext text/x-wiki One of the most frequent errors with uploading the data is incorrect file format. We recommend fasta format for all the sequence data to be uploaded. In particular, please check the following things: # There should be no spaces or tabs at the start or ends of the lines # The identifier line should begin with a greater than sign ">", and only one line is allowed # Typically most bioinformatics applications use the first word after the > as the identifier for the sequence. Its nice (but not essential) if this is unique # In the sequence lines (not header lines), spaces and numbers are removed. Examples of valid fasta >sequenceid gatgcagcatgcagctagcagcgacggactac... >1 this is a sequence that i know something about gatgcagcatgcagctagcagcgacggactac... Examples of invalid fasta >sequenceid This is a comment about the sequence gatgcagcatgcagctagcagcgacggactac... ''Pleae don't include comments in the sequence data'' >sequenceid gatgcagcatgcagctagcagcgacggactac... ''please don't have spaces before the > in the identifier'' fasta is probably the most common sequence format because it is relatively compact, and very easy to parse. There is more information about the fasta format at: # [http://en.wikipedia.org/wiki/Fasta_format Wikipedia] # [http://www.ncbi.nlm.nih.gov/blast/fasta.shtml NCBI] ba380428c797076e29ff4cc5ad19cbad74c1ddd3 1728 1727 2007-10-04T18:54:28Z RobEdwards 14 wikitext text/x-wiki One of the most frequent errors with uploading the data is incorrect file format. We recommend fasta format for all the sequence data to be uploaded. In particular, please check the following things: # There should be no spaces or tabs at the start or ends of the lines # The identifier line should begin with a greater than sign ">", and only one line is allowed # Typically most bioinformatics applications use the first word after the > as the identifier for the sequence. Its nice (but not essential) if this is unique # In the sequence lines (not header lines), spaces and numbers are removed. Examples of valid fasta >sequenceid gatgcagcatgcagctagcagcgacggactac... >1 this is a sequence that i know something about gatgcagcatgcagctagcagcgacggactac... Examples of invalid fasta >sequenceid This is a comment about the sequence gatgcagcatgcagctagcagcgacggactac... ''Pleae don't include comments in the sequence data'' >sequenceid gatgcagcatgcagctagcagcgacggactac... ''please don't have spaces before the > in the identifier'' fasta is probably the most common sequence format because it is relatively compact, and very easy to parse. There is more information about the fasta format at: # [http://en.wikipedia.org/wiki/Fasta_format Wikipedia] # [http://www.ncbi.nlm.nih.gov/blast/fasta.shtml NCBI] a9c558d7f2484e9193a4f2616b32e54f285bca4d 0 1437 1730 2007-10-04T19:16:05Z RobEdwards 14 Which sequences should be uploaded to the RAST or MG-RAST services wikitext text/x-wiki == Which Seqeunces Should I Upload? == We have different options for publicly available sequence analysis, and some can take different types of sequence data: # The [[#Metagenomics Rast Server |Metagenomics RAST Server]] for metagenome sequences # The [[#RAST Server|RAST Server]] for complete genomes Please note, that most of our users problems are because the sequences are # Not in [[Valid fasta format]] # Not nucleotide sequences. At the moment we don't have any service for annotating just protein sequences. If there is a large demand, we can add this, but you probably don't want to use genome annotation tools to annotate protein sequnces anyway. === Metagenomics Rast Server === The [http://metagenomics.nmpdr.org/ Metagenomics RAST Server] is designed to annotate '''nucleotide''' sequences from metagenome projects. You can supply either assembled or unassembled data, and reads can be as short as 100 bp and as long as you would like. There are some caveats to the system: ==== Unassembled Data ==== If you want to do statistical comparisons between metagenomes, you most likely need unassembled sequences. The frequency that any gene is found is an approximation of the abundance of that gene in the environment. Thus if you two different samples you can compare gene frequencies between them to figure out which are the important environments. In this case, just upload the unassembled '''nucleotide''' sequences in [[Valid fasta format]] ==== Assembled Data ==== If you want to look for complete genes or pieces of a genome, then you can use assembled sequences. These are typically longer, and the ORF caller we use on the short fragments and sequences may have problems with longer sequences. On the ''to do list'' is to add specific ORF callers for different sequence sets. For sequences over about 1,000,000 bp (1 Mbp) you should consider pulling out those sequences individually and running them through the [[#RAST Server|RAST Server]] server for complete genomes. This server uses far superior gene identification and analysis algorithms that are only applicable once you have longer sequences. However, the algorithm will not work very well with sequences under about 1 Mbp. If you assemble sequences you will loose the frequency information, and cannot easily do statistical comparisons between metagenomes. === RAST Server === The [http://www.nmpdr.org/anno-server RAST Server] is designed for complete, or nearly complete, microbial genomes. This uses a novel form of gene calling based on protein families, that is described in our upcoming paper. One of the basics of this technique is understanding where your organism lies using phylogenomics to ensure that we get accurate ORF calling. It doesn't make sense to use this technique for metagenomics. Furthermore, the RAST Server also leverages the SEED's work on functional coupling, assigning functions based on nearby genes. The RAST Server is currently the best annotation platform for complete genomes. == Remember! == Remember: * '''nucleotides only''' * '''[Valid fasta format''' * Metagenomes, assembled or unassembled, use the [http://metagenomics.nmpdr.org/ Metagenomics RAST Server] * Complete genomes, or nearly complete (to the order of tens of contigs), use the [http://www.nmpdr.org/anno-server RAST Server] af1af291989e39f95c8478e2f211791f1715220d 1731 1730 2007-10-04T19:16:48Z RobEdwards 14 /* Remember! */ wikitext text/x-wiki == Which Seqeunces Should I Upload? == We have different options for publicly available sequence analysis, and some can take different types of sequence data: # The [[#Metagenomics Rast Server |Metagenomics RAST Server]] for metagenome sequences # The [[#RAST Server|RAST Server]] for complete genomes Please note, that most of our users problems are because the sequences are # Not in [[Valid fasta format]] # Not nucleotide sequences. At the moment we don't have any service for annotating just protein sequences. If there is a large demand, we can add this, but you probably don't want to use genome annotation tools to annotate protein sequnces anyway. === Metagenomics Rast Server === The [http://metagenomics.nmpdr.org/ Metagenomics RAST Server] is designed to annotate '''nucleotide''' sequences from metagenome projects. You can supply either assembled or unassembled data, and reads can be as short as 100 bp and as long as you would like. There are some caveats to the system: ==== Unassembled Data ==== If you want to do statistical comparisons between metagenomes, you most likely need unassembled sequences. The frequency that any gene is found is an approximation of the abundance of that gene in the environment. Thus if you two different samples you can compare gene frequencies between them to figure out which are the important environments. In this case, just upload the unassembled '''nucleotide''' sequences in [[Valid fasta format]] ==== Assembled Data ==== If you want to look for complete genes or pieces of a genome, then you can use assembled sequences. These are typically longer, and the ORF caller we use on the short fragments and sequences may have problems with longer sequences. On the ''to do list'' is to add specific ORF callers for different sequence sets. For sequences over about 1,000,000 bp (1 Mbp) you should consider pulling out those sequences individually and running them through the [[#RAST Server|RAST Server]] server for complete genomes. This server uses far superior gene identification and analysis algorithms that are only applicable once you have longer sequences. However, the algorithm will not work very well with sequences under about 1 Mbp. If you assemble sequences you will loose the frequency information, and cannot easily do statistical comparisons between metagenomes. === RAST Server === The [http://www.nmpdr.org/anno-server RAST Server] is designed for complete, or nearly complete, microbial genomes. This uses a novel form of gene calling based on protein families, that is described in our upcoming paper. One of the basics of this technique is understanding where your organism lies using phylogenomics to ensure that we get accurate ORF calling. It doesn't make sense to use this technique for metagenomics. Furthermore, the RAST Server also leverages the SEED's work on functional coupling, assigning functions based on nearby genes. The RAST Server is currently the best annotation platform for complete genomes. == Remember! == Remember: * '''nucleotides only''' * '''[[Valid fasta format]]''' * Metagenomes, assembled or unassembled, use the [http://metagenomics.nmpdr.org/ Metagenomics RAST Server] * Complete genomes, or nearly complete (to the order of tens of contigs), use the [http://www.nmpdr.org/anno-server RAST Server] 81563a10d22dbb6112409b6e14effb7117cf1965 1732 1731 2007-10-04T19:18:25Z RobEdwards 14 /* Which Seqeunces Should I Upload? */ wikitext text/x-wiki == Which Seqeunces Should I Upload? == We have different options for publicly available sequence analysis, and some can take different types of sequence data: # The [[#Metagenomics Rast Server |Metagenomics RAST Server]] for metagenome sequences # The [[#RAST Server|RAST Server]] for complete genomes Please note, that most of our users problems are because the sequences are # Not in [[Valid fasta format]] # Not nucleotide sequences. At the moment we don't have any service for annotating just protein sequences. If there is a large demand, we can add this, but you probably don't want to use genome annotation tools to annotate protein sequences anyway. === Metagenomics Rast Server === The [http://metagenomics.nmpdr.org/ Metagenomics RAST Server] is designed to annotate '''nucleotide''' sequences from metagenome projects. You can supply either assembled or unassembled data, and reads can be as short as 100 bp and as long as you would like. There are some caveats to the system: ==== Unassembled Data ==== If you want to do statistical comparisons between metagenomes, you most likely need unassembled sequences. The frequency that any gene is found is an approximation of the abundance of that gene in the environment. Thus if you two different samples you can compare gene frequencies between them to figure out which are the important environments. In this case, just upload the unassembled '''nucleotide''' sequences in [[Valid fasta format]] ==== Assembled Data ==== If you want to look for complete genes or pieces of a genome, then you can use assembled sequences. These are typically longer, and the ORF caller we use on the short fragments and sequences may have problems with longer sequences. On the ''to do list'' is to add specific ORF callers for different sequence sets. For sequences over about 1,000,000 bp (1 Mbp) you should consider pulling out those sequences individually and running them through the [[#RAST Server|RAST Server]] server for complete genomes. This server uses far superior gene identification and analysis algorithms that are only applicable once you have longer sequences. However, the algorithm will not work very well with sequences under about 1 Mbp. If you assemble sequences you will loose the frequency information, and cannot easily do statistical comparisons between metagenomes. === RAST Server === The [http://www.nmpdr.org/anno-server RAST Server] is designed for complete, or nearly complete, microbial genomes. This uses a novel form of gene calling based on protein families, that is described in our upcoming paper. One of the basics of this technique is understanding where your organism lies using phylogenomics to ensure that we get accurate ORF calling. It doesn't make sense to use this technique for metagenomics. Furthermore, the RAST Server also leverages the SEED's work on functional coupling, assigning functions based on nearby genes. The RAST Server is currently the best annotation platform for complete genomes. == Remember! == Remember: * '''nucleotides only''' * '''[[Valid fasta format]]''' * Metagenomes, assembled or unassembled, use the [http://metagenomics.nmpdr.org/ Metagenomics RAST Server] * Complete genomes, or nearly complete (to the order of tens of contigs), use the [http://www.nmpdr.org/anno-server RAST Server] f22c9e18ce2112652d7f147968b9b48c9af68f93 1734 1732 2007-10-05T07:27:18Z RobEdwards 14 /* Metagenomics Rast Server */ wikitext text/x-wiki == Which Seqeunces Should I Upload? == We have different options for publicly available sequence analysis, and some can take different types of sequence data: # The [[#Metagenomics Rast Server |Metagenomics RAST Server]] for metagenome sequences # The [[#RAST Server|RAST Server]] for complete genomes Please note, that most of our users problems are because the sequences are # Not in [[Valid fasta format]] # Not nucleotide sequences. At the moment we don't have any service for annotating just protein sequences. If there is a large demand, we can add this, but you probably don't want to use genome annotation tools to annotate protein sequences anyway. === Metagenomics Rast Server === The [http://metagenomics.nmpdr.org/ Metagenomics RAST Server] is designed to annotate '''nucleotide''' sequences from metagenome projects. You can supply either assembled or unassembled data, and reads can be as short as 100 bp and as long as you would like. There are some caveats to the system. Please also read this explanation of appropriate [[metagenomics sequence formats]]. ==== Unassembled Data ==== If you want to do statistical comparisons between metagenomes, you most likely need unassembled sequences. The frequency that any gene is found is an approximation of the abundance of that gene in the environment. Thus if you two different samples you can compare gene frequencies between them to figure out which are the important environments. In this case, just upload the unassembled '''nucleotide''' sequences in [[Valid fasta format]] ==== Assembled Data ==== If you want to look for complete genes or pieces of a genome, then you can use assembled sequences. These are typically longer, and the ORF caller we use on the short fragments and sequences may have problems with longer sequences. On the ''to do list'' is to add specific ORF callers for different sequence sets. For sequences over about 1,000,000 bp (1 Mbp) you should consider pulling out those sequences individually and running them through the [[#RAST Server|RAST Server]] server for complete genomes. This server uses far superior gene identification and analysis algorithms that are only applicable once you have longer sequences. However, the algorithm will not work very well with sequences under about 1 Mbp. If you assemble sequences you will loose the frequency information, and cannot easily do statistical comparisons between metagenomes. === RAST Server === The [http://www.nmpdr.org/anno-server RAST Server] is designed for complete, or nearly complete, microbial genomes. This uses a novel form of gene calling based on protein families, that is described in our upcoming paper. One of the basics of this technique is understanding where your organism lies using phylogenomics to ensure that we get accurate ORF calling. It doesn't make sense to use this technique for metagenomics. Furthermore, the RAST Server also leverages the SEED's work on functional coupling, assigning functions based on nearby genes. The RAST Server is currently the best annotation platform for complete genomes. == Remember! == Remember: * '''nucleotides only''' * '''[[Valid fasta format]]''' * Metagenomes, assembled or unassembled, use the [http://metagenomics.nmpdr.org/ Metagenomics RAST Server] * Complete genomes, or nearly complete (to the order of tens of contigs), use the [http://www.nmpdr.org/anno-server RAST Server] 42cb7132524dbae3f881172388ea4caad370ed26 1739 1734 2007-10-05T07:47:22Z RobEdwards 14 /* Which Seqeunces Should I Upload? */ wikitext text/x-wiki == Which Seqeunces Should I Upload? == We have different options for publicly available sequence analysis, and some can take different types of sequence data: # The [[#Metagenomics Rast Server |Metagenomics RAST Server]] for metagenome sequences # The [[#RAST Server|RAST Server]] for complete genomes Please note, that most of our users problems are because the sequences are # Not in [[Valid fasta format]] # Not in the right [[Metagenomics sequence formats|file formats]] # Not nucleotide sequences. At the moment we don't have any service for annotating just protein sequences. If there is a large demand, we can add this, but you probably don't want to use genome annotation tools to annotate protein sequences anyway. === Metagenomics Rast Server === The [http://metagenomics.nmpdr.org/ Metagenomics RAST Server] is designed to annotate '''nucleotide''' sequences from metagenome projects. You can supply either assembled or unassembled data, and reads can be as short as 100 bp and as long as you would like. There are some caveats to the system. Please also read this explanation of appropriate [[metagenomics sequence formats]]. ==== Unassembled Data ==== If you want to do statistical comparisons between metagenomes, you most likely need unassembled sequences. The frequency that any gene is found is an approximation of the abundance of that gene in the environment. Thus if you two different samples you can compare gene frequencies between them to figure out which are the important environments. In this case, just upload the unassembled '''nucleotide''' sequences in [[Valid fasta format]] ==== Assembled Data ==== If you want to look for complete genes or pieces of a genome, then you can use assembled sequences. These are typically longer, and the ORF caller we use on the short fragments and sequences may have problems with longer sequences. On the ''to do list'' is to add specific ORF callers for different sequence sets. For sequences over about 1,000,000 bp (1 Mbp) you should consider pulling out those sequences individually and running them through the [[#RAST Server|RAST Server]] server for complete genomes. This server uses far superior gene identification and analysis algorithms that are only applicable once you have longer sequences. However, the algorithm will not work very well with sequences under about 1 Mbp. If you assemble sequences you will loose the frequency information, and cannot easily do statistical comparisons between metagenomes. === RAST Server === The [http://www.nmpdr.org/anno-server RAST Server] is designed for complete, or nearly complete, microbial genomes. This uses a novel form of gene calling based on protein families, that is described in our upcoming paper. One of the basics of this technique is understanding where your organism lies using phylogenomics to ensure that we get accurate ORF calling. It doesn't make sense to use this technique for metagenomics. Furthermore, the RAST Server also leverages the SEED's work on functional coupling, assigning functions based on nearby genes. The RAST Server is currently the best annotation platform for complete genomes. == Remember! == Remember: * '''nucleotides only''' * '''[[Valid fasta format]]''' * Metagenomes, assembled or unassembled, use the [http://metagenomics.nmpdr.org/ Metagenomics RAST Server] * Complete genomes, or nearly complete (to the order of tens of contigs), use the [http://www.nmpdr.org/anno-server RAST Server] e2687d798f60d3f03e1919475f43a5b8322ea695 1740 1739 2007-10-05T07:47:43Z RobEdwards 14 /* Which Seqeunces Should I Upload? */ wikitext text/x-wiki == Which Seqeunces Should I Upload? == We have different options for publicly available sequence analysis, and some can take different types of sequence data: # The [[#Metagenomics Rast Server |Metagenomics RAST Server]] for metagenome sequences # The [[#RAST Server|RAST Server]] for complete genomes Please note, that most of our users problems are because the sequences are # Not in [[Valid fasta format]] # Not the right [[Metagenomics sequence formats|file formats]] # Not nucleotide sequences. At the moment we don't have any service for annotating just protein sequences. If there is a large demand, we can add this, but you probably don't want to use genome annotation tools to annotate protein sequences anyway. === Metagenomics Rast Server === The [http://metagenomics.nmpdr.org/ Metagenomics RAST Server] is designed to annotate '''nucleotide''' sequences from metagenome projects. You can supply either assembled or unassembled data, and reads can be as short as 100 bp and as long as you would like. There are some caveats to the system. Please also read this explanation of appropriate [[metagenomics sequence formats]]. ==== Unassembled Data ==== If you want to do statistical comparisons between metagenomes, you most likely need unassembled sequences. The frequency that any gene is found is an approximation of the abundance of that gene in the environment. Thus if you two different samples you can compare gene frequencies between them to figure out which are the important environments. In this case, just upload the unassembled '''nucleotide''' sequences in [[Valid fasta format]] ==== Assembled Data ==== If you want to look for complete genes or pieces of a genome, then you can use assembled sequences. These are typically longer, and the ORF caller we use on the short fragments and sequences may have problems with longer sequences. On the ''to do list'' is to add specific ORF callers for different sequence sets. For sequences over about 1,000,000 bp (1 Mbp) you should consider pulling out those sequences individually and running them through the [[#RAST Server|RAST Server]] server for complete genomes. This server uses far superior gene identification and analysis algorithms that are only applicable once you have longer sequences. However, the algorithm will not work very well with sequences under about 1 Mbp. If you assemble sequences you will loose the frequency information, and cannot easily do statistical comparisons between metagenomes. === RAST Server === The [http://www.nmpdr.org/anno-server RAST Server] is designed for complete, or nearly complete, microbial genomes. This uses a novel form of gene calling based on protein families, that is described in our upcoming paper. One of the basics of this technique is understanding where your organism lies using phylogenomics to ensure that we get accurate ORF calling. It doesn't make sense to use this technique for metagenomics. Furthermore, the RAST Server also leverages the SEED's work on functional coupling, assigning functions based on nearby genes. The RAST Server is currently the best annotation platform for complete genomes. == Remember! == Remember: * '''nucleotides only''' * '''[[Valid fasta format]]''' * Metagenomes, assembled or unassembled, use the [http://metagenomics.nmpdr.org/ Metagenomics RAST Server] * Complete genomes, or nearly complete (to the order of tens of contigs), use the [http://www.nmpdr.org/anno-server RAST Server] 76dfebe7b8b5f20513519b85ad5f3a02d02e9673 0 1438 1736 2007-10-05T07:45:00Z RobEdwards 14 What files to upload wikitext text/x-wiki == File formats == To upload sequence data to the metagenomics RAST server, we accept several file formats. * You can upload a fasta file containing ''just the nucleotide sequences''. This is the simplest format, just have a regular [[Valid fasta format]] nucleotide sequence file, and upload it. However, there may be some limitation on the file size. * You can compress the sequence file containing ''just the nucleotide sequences'' with [http://www.gzip.org/ gzip], a popular compression tool. This will significantly reduce the size of the file to upload, and hence speed things up. * You can also include a ''separate'' quality file in this same compressed file. To do this, compress both files into a single archive: gzip archive.gz sequence.fa sequence.qual and then upload the archive.gz file (don't worry, we'll take care of the name!) If you do this, we will renumber the sequences and their corresponding quality scores at the same time. At the moment we don't use the quality scores, although we are experimenting with assembly tools that may take advantage of them. Therefore, the inclusion of quality scores is completely optional. 5d3ed72252e4a8a6022a2edbf49bec5a8cb92b16 1737 1736 2007-10-05T07:45:37Z RobEdwards 14 /* File formats */ wikitext text/x-wiki == File formats == To upload sequence data to the metagenomics RAST server, we accept several file formats. * You can upload a fasta file containing ''just the nucleotide sequences''. This is the simplest format, just have a regular [[Valid fasta format]] nucleotide sequence file, and upload it. However, there may be some limitation on the file size. * You can compress the sequence file containing ''just the nucleotide sequences'' with [http://www.gzip.org/ gzip], a popular compression tool. This will significantly reduce the size of the file to upload, and hence speed things up. * You can also include a ''separate'' quality file in this same compressed file. To do this, compress both files into a single archive and then upload the archive.gz file (don't worry, we'll take care of the name, you can call it whatever you want!): gzip archive.gz sequence.fa sequence.qual If you do this, we will renumber the sequences and their corresponding quality scores at the same time. At the moment we don't use the quality scores, although we are experimenting with assembly tools that may take advantage of them. Therefore, the inclusion of quality scores is completely optional. fb2a10087013c0a4a76ede94ef47a0c7a2d34b5a 1738 1737 2007-10-05T07:46:21Z RobEdwards 14 /* File formats */ wikitext text/x-wiki == File formats == To upload sequence data to the metagenomics RAST server, we accept several file formats. * You can upload a fasta file containing '''just the nucleotide sequences'''. This is the simplest format, just have a regular [[Valid fasta format]] nucleotide sequence file, and upload it. However, there may be some limitation on the file size. * You can compress the sequence file containing '''just the nucleotide sequences''' with [http://www.gzip.org/ gzip], a popular compression tool. This will significantly reduce the size of the file to upload, and hence speed things up. * You can also include a '''separate''' quality file in this same compressed file. To do this, compress both files into a single archive and then upload the archive.gz file (don't worry, we'll take care of the name, you can call it whatever you want!): gzip archive.gz sequence.fa sequence.qual If you do this, we will renumber the sequences and their corresponding quality scores at the same time. At the moment we don't use the quality scores, although we are experimenting with assembly tools that may take advantage of them. Therefore, the inclusion of quality scores is completely optional. c59d3ffefbad1082e4a0bd87a8f5bec7bcf8a19c 1741 1738 2007-10-05T07:48:38Z RobEdwards 14 /* File formats */ wikitext text/x-wiki == Common Errors == Please note, that most of our users problems are because the sequences are # Not in [[Valid fasta format]] # Not the right [[Metagenomics sequence formats|file formats]] # Not nucleotide sequences. At the moment we don't have any service for annotating just protein sequences. If there is a large demand, we can add this, but you probably don't want to use genome annotation tools to annotate protein sequences anyway. # See also [[Which Sequences Should I Upload, and Where]] == File formats == To upload sequence data to the metagenomics RAST server, we accept several file formats. * You can upload a fasta file containing '''just the nucleotide sequences'''. This is the simplest format, just have a regular [[Valid fasta format]] nucleotide sequence file, and upload it. However, there may be some limitation on the file size. * You can compress the sequence file containing '''just the nucleotide sequences''' with [http://www.gzip.org/ gzip], a popular compression tool. This will significantly reduce the size of the file to upload, and hence speed things up. * You can also include a '''separate''' quality file in this same compressed file. To do this, compress both files into a single archive and then upload the archive.gz file (don't worry, we'll take care of the name, you can call it whatever you want!): gzip archive.gz sequence.fa sequence.qual If you do this, we will renumber the sequences and their corresponding quality scores at the same time. At the moment we don't use the quality scores, although we are experimenting with assembly tools that may take advantage of them. Therefore, the inclusion of quality scores is completely optional. 344d0b79c238425f4a1596381efe826bb8f44c16 1751 1741 2007-11-04T19:36:11Z RobEdwards 14 wikitext text/x-wiki == Common Errors == Please note, that most of our users problems are because the sequences are # Not in [[Valid fasta format]] # Not the right [[Metagenomics sequence formats|file formats]] # Not nucleotide sequences. At the moment we don't have any service for annotating just protein sequences. If there is a large demand, we can add this, but you probably don't want to use genome annotation tools to annotate protein sequences anyway. # See also [[Which Sequences Should I Upload, and Where]] == File formats == To upload sequence data to the metagenomics RAST server, we accept several file formats. * You can upload a fasta file containing '''just the nucleotide sequences'''. This is the simplest format, just have a regular [[Valid fasta format]] nucleotide sequence file, and upload it. However, there may be some limitation on the file size. In this case the file name should end .fa, .fasta, or .fna. * You can compress the sequence file containing '''just the nucleotide sequences''' with tar and gzip a popular compression tool. This will significantly reduce the size of the file to upload, and hence speed things up. In this case the file name should end .tgz and the fasta file should end .fa, .fasta, or .fna. * You can also include a '''separate''' quality file in this same compressed file. To do this, compress both files into a single archive and then upload the archive.tgz file (don't worry, we'll take care of the name, you can call it whatever you want!): tar zcf archive.tgz sequence.fa sequence.qual If you do this, we will renumber the sequences and their corresponding quality scores at the same time. At the moment we don't use the quality scores, although we are experimenting with assembly tools that may take advantage of them. Therefore, the inclusion of quality scores is completely optional. * Please note that at the moment we only accept tar/gzipped compressed formats, and if you upload other formats the upload will fail. Sorry. 9a26ee9500bb413f778c15a8b4ed173dfa63e325 0 1439 1742 2007-10-05T20:04:23Z TobiasPaczian 17 wikitext text/x-wiki The SeedViewer, RAST-Server and MG-RAST-Server were developed in an Web Application Framework developed by Daniel Paarmann and Tobias Paczian. Here you will find the links to tutorials and documentation. * [[Web Application]] * [[Web Components]] * [[Persistant Perl Objects]] fec95037b2c0de1e41f2eaa1a4980bdd86f414e1 1749 1742 2007-10-05T20:09:35Z TobiasPaczian 17 wikitext text/x-wiki The SeedViewer, RAST-Server and MG-RAST-Server were developed in an Web Application Framework developed by Daniel Paarmann and Tobias Paczian. Here you will find the links to tutorials and documentation. * [[Web Application]] * [[Web Components]] * [[Persistent Perl Objects]] 51e324a356b16508859a8b476b9d04b7403ea8b5 0 1440 1743 2007-10-05T20:04:45Z TobiasPaczian 17 wikitext text/x-wiki The Web Application is a framework to support fast, comprehesible and componentalized creation of applications on the web. == Overview == The Web Application framework will take care of the structure of your application in the web. Main features include: * menus * user authentication * page/action management * WebComponents The following tutorial will describe how to set up your own application in the web using the WebApplication framework. == Setup == There are two modules required for the Web Application framework: * WebApplication * PPO both must be checked out from the CVS. The following assumes you have set up a sandbox for your application. If you do not know how to set up a sandbox have bob do it ;) or go to [[Sandbox Setup]]. cd ~/public_html/my-app/dist/releases/current/ cvs co WebApplication cvs co PPO Now create a directory for your application. mkdir MyApp cd MyApp Now we fill in the neccessary elements that customize your application. You need to create the following things: * a '''cgi-script''' that becomes the centerpoint for your application * a '''directory''' called '''WebPage''' that will contain your different pages * an '''initial page''' for your application to display * a '''template file''' that describes the layout of your pages (optional) * a '''stylesheet''' that takes care of font-styles and the like (optional) * a '''directory''' for the '''images''' you want on your pages (optional) To get things going, perform the following steps: cp ../WebApplication/example/example.cgi myApp.cgi cp ../WebApplication/example/Example.Makefile Makefile mkdir WebPage cp ../WebApplication/example/Example.pm WebPage/MyFirstPage.pm cp ../WebApplication/WebLayoutDefault.tmpl MyAppLayout.tmpl mkdir images cd images cp ../../WebApplication/images/* . As you can see, there are example files for all of these that you can modify. At this point, your application is already up and running. Do a '''make''' and examine the result in the web: http://bioseed.mcs.anl.gov/~juser/my-app/www/FIG/myApp.cgi [[Image:MyFirstApp.png]] The WebApplication comes with a default stylesheet (css) that defines colours and fonts and so on. It's likely that you want change those at some point. To do so: go back to your working application directory: cd MyApp mkdir css cp ../WebApplication/css/default.css css/myapp.css Now edit your myApp.cgi and replace the css filename in the following line: $layout->add_css(TMPL_PATH.'/myapp.css'); == Your First Page == This is the demo page you have copied from the WepApplication directory. All it will do is print a page that reads 'Hello World'. When you go to the url of your application's script, this is the first page that will appear. This is because in the [[Web Application Script]] it is defined as the default first page. package MyApp::WebPage::MyFirstPage; use strict; use warnings; use base qw( WebPage ); 1; sub output { my ($self) = @_; my $content = "&lt;h1>Hello World&lt;/h1>"; return $content; } The logic of the Web Application will perform the following checks to see which page should be displayed: * was the cgi parameter '''page''' passed? ** '''Yes:''' check if the page '''$cgi->param('page')''' requires any rights to be displayed *** if there are no rights required, display the page *** if there are rights required and there is no user, display the login page. After the login page has been processed, recheck to display this page. *** if there are rights required and the user does not possess them, display an error *** if there are rights required and the user does possess them, display the page ** '''No:''' display the default first page *** perform same authorization steps === Creating a new Page === If you wish to create a new page, simply create a new file in the '''WebPage''' directory of your application. You can copy the example file from the WebApplication directory as a template. cd ~/public_html/myApp/dist/releases/current/myApp/WebPage/ cp ../WebApplication/Example.pm MyNewPage.pm The name of the file, will be the value of the cgi page parameter which will display your page. http://bioseed.mcs.anl.gov/~juser/myApp/www/FIG/myApp.cgi?page=MyNewPage Would point to your new page. === Page Methods === When inside the your page module, you can access the inherited '''WebPage''' methods using $self->method(params); The following methods are available. * '''title''' (string) Sets the title information for this page. This will be displayed in the title bar of your browser. * '''application''' Returns the application object. * '''name''' Returns the name of the current page. * '''url''' Returns the url to the current page. * '''start_form''' (string, hashref) Returns an opening html form tag. The string passed will be the html id of the form ''(optional)''. The hash reference is used to preserve the current state. The keys will be inserted as '''hidden''' fields with their values set to the values of the according hash entry. * '''end_form''' Returns a closing html form tag. The following are abstract functions which you can implement in your page. * '''init''' This should include all functionality which must be called ''prior'' to calling the '''output''' method of the page. Component registration using <br> :'''$self->application->register_component('ComponentType', 'ComponentID');'''<br> is an example of this. * '''require_javascript''' This must return an array reference. Each element in the array must be the filename of a java script file. This file will automatically be included in the header of the page. If this method is not implemented, no extra java script will be included for this page. * '''require_css''' This must return a string which must be the filename of the stylesheet file to be included for this page. If this method is not implementd, no extra stylesheet will be included for this page. * '''required_rights''' This must return an arrayref of arrayrefs. Each element in the array must be a rights tuple. These are explained in the [[Using Rights]] section. If this method is not implemented, no rights will be required to see this page. === Application Methods === Since every page you create inherits from '''WebPage''', you can access the application object using my $application = $self->application; The '''application object''' then offers the following functions * '''session''' This will return the '''session object'''. The session object then allows access to the following functions :* '''user''' :Returns the '''user object''' :* '''get_entry''' :Returns the name and parameters of the page last visited. * '''cgi''' Returns the '''cgi object''' * '''error''' Sets the applications error message. This will cause an error page to be displayed. No other content will be seen on the page. If you wish to display the normal content of the page and in addition some note to the user, you can use the '''add_message''' method. * '''add_message''' Adds a note or a warning to the page. This method takes two arguments, the first one can be either 'warning' or 'info', depending on which type of message you wish to add. The second parameter is the actual message. * '''page''' Returns the current page object. * '''url''' Returns the script url * '''redirect''' Causes the url passed to be loaded instead of the current one. * '''register_component''' Registers a component at the application. This component can be retrieved via the '''component' method. * '''component''' Retrieves a previously requested component object. * '''register_action''' Registers an action for this page with the application. If an unregistered action is called, an error will occur. The following functions are usually only used in the [[Web Application Script]] of your application. * '''default''' Sets the default first page to load if no cgi page parameter is given. * '''dbmaster''' Sets the database master which will be used to crud user and session information. * '''layout''' Sets the WebLayout used to build the application pages. ==== Menus ==== * '''menu''' Returns the '''menu object'''. The menu object then allows access to the following functions :* '''add_category''' (category, url, target, right, sort_order) :* '''delete_category''' (category) :* '''get_categories''' :* '''add_entry''' (category, entry, url, target) === Using Rights === The WebApplication also offers you the ability of '''Rights Management'''. This topic is described in detail at the [[WebApplication Rights]] page. == [[Web Components]] == The ability to include standard components into your application is one of the main features of the Web Application framework. This will give you a short introduction on how to use these components. A comprehesive list with detailed feature descriptions of currently available components is available on the [[Web Components]] page. There are two methods of the application object that refer to components. $application->register_component('ComponentName', 'ComponentID'); my $component = $application->component('ComponentID'); The first one registers a component for your page. This means an actual instance of the component type you request is created and stored in the application. This instance can now be accessed by the second method by passing the ID you chose for this component instance. The registration of a component must be done in a pages '''init''' method. After retrieving the requested component from the application object, you can then access its methods. Typically, components have '''getter/setter''' functions to set their parameters and an '''output''' method to return html content you can print onto your page. The following code is using the Login component as an example. sub init { my $self = shift; $self->application->register_component('Login', 'MyLogin'); } sub output { my ($self) = @_; my $content = ""; my $application = $self->application; my $cgi = $application->cgi; my $login_component = $application->component('MyLogin'); $login_component->small_login(1); my $login = $login_component->output; $content .= "&lt;h1>Hello World&lt;/h1>" . $login; return $content; } == Advanced Customizing == If you are merely designing an manipulating pages, there is no need for you to ever look at any files outside the '''WebPage''' directory of you application. If you are setting up the application however, you need to check the [[Web Application Template]] and the [[Web Application Script]]. There are also '''Stylesheets''' that you can modify and you probably wish to exchange some '''images''', like the logo. e3a1b4bd514ac5ee069ee054ae4b012926fffe31 0 1441 1744 2007-10-05T20:05:37Z TobiasPaczian 17 wikitext text/x-wiki Web Components are self contained objects that produce html output for standard application components that can be used in the context of a [[Web Application]]. == Overview == Here you will find a comprehensive list of the currently available Web Components and their parameters. To include a Web Component in your application, follow the instructions on the [[Web Application]] page. == Component List == === Table === In its simplest form, this merely displays a table. The component also offers the functionality for column sorting, column filtering, browsing, highlighting, onclick-events for cells, popup menus for cells and an export function. '''Example''' [[Image:Example_table.png]] This table was created using the following code $self->application->register_component('Table', 'testtable'); my $table_component = $self->application->component('testtable'); $table_component->data([ ['A','B','C'], ['D','E','F'], ['G','H','I'] ]); $table_component->columns( [ { 'name' => 'Col A', 'filter' => 1 }, { 'name' => 'Col B' }, { 'name' => 'Col C', 'filter' => 1, 'operators' => [ 'like', 'unlike' ] } ] ); $table_component->show_top_browse(1); $table_component->show_bottom_browse(1); $table_component->items_per_page(2); $table_component->show_select_items_per_page(1); print $table_component->output(); '''Parameters''' * '''data''' (arrayref of arrayrefs of strings) The table data must be a list of rows, each of which is a list of cells. For each cell you have two options. :* ''pass a string'' - this string will then become the content of the cell :* ''pass a hash'' - the hash allows you to pass additional options: ::* '''data''' - the data of the cell ::* '''highlight''' - an integer defining the highlight color of the cell: :::The integers represent different highlighting colors :::* 0: no highlighting :::* 1: green :::* 2: blue :::* 3: red :::* 4: yellow ::* '''menu''' - a menu as used in the Hover component described below. This must be a hash with the keys 'titles' and 'links', each pointing to array references with the according entries for the titles and the links of the menu ::* '''tooltip''' - html to be displayed in the tooltip of this cell. ::* '''onclick''' - the url the onclick event of the cell should take the page to * '''columns''' (arrayref of (hashrefs or strings)) : If you do not pass hashrefs, the strings will be used as the column header :* ''name:'' the text in the column header :* ''sortable:'' a boolean indicating whether clicking the column header will sort this column. The sort function will determine the kind of data given the first cell of the column. Recognized data types are: ::* ''date'': /^\d\d[\/-]\d\d[\/-]\d\d\d\d$/ or /^\d\d[\/-]\d\d[\/-]\d\d$/ ::* ''numerical'': /^\d+\.{0,1}\d*$/ ::* ''e-value'': /^\d+\.{1}\d+e[+-]{1}\d+$/ ::* ''alphabetical'': everything unrecognized by the above :* ''filter:'' a boolean indicating whether this column should have a filter box :* ''operator:'' the operator the filter will use by default. May be either one of: '''like''', '''unlike''', '''equal''', '''unequal''', '''less''', '''more'''. You can also set the operator to '''combobox''' which will create a combobox as a filter, filled with every distinct value of that column. :* ''operators:'' the selection of operators the user may choose from when filtering. This must be an array of the above. Each element in the columns array represents one column. These elements may have several properties, only '''name'' being mandatory. :* ''width:'' the width of the column in pixels. :* ''visible:'' a boolean indicating whether this column is to be displayed. Invisible columns will be added to the control panel. :* ''show_control:'' a boolean indicating whether to display this column in a control panel above the table. The column headers of those columns will appear in the control panel, allowing to sort/filter the columns, without the need of displaying them. '''Options''' * '''items_per_page''' (int) Determines the number of rows that will be displayed at a time. If you specify this, you should choose at least one of the browse options, so the user can browse through the data. * '''show_export_button''' (boolean or hash) If this is a boolean, then a value of true will display a button to export the table above the table. If this is a hash, you have multiple options for the export button: :* '''title''': the title of the button :* '''strip_html''': The export will strip any html tags from cells before exporting :* '''unfiltered''': Instead of the normal behavior, where only the cells that passed the current filter will be exported, all cells are exported :* '''hide_invisible_columns''': All cells in columns currently marked as invisible will not be exported * '''show_select_items_per_page''' (boolean) If true will allow the user to select how many rows should be displayed at a time. * '''show_top_browse''' (boolean) If true will display browsing functions above the table. * '''show_bottom_browse''' (boolean) If true will display browsing functions below the table. * '''offset''' (int) The number of rows that will initially not be show from the beginning of the dataset. * '''width''' (int) The width of the table in pixels. '''Additional Functions''' The table module supports a set of javascript functions for manipulation. * '''show_column''' (table_id, colum_index) This will make a column in the table visible. * '''hide_column''' (table_id, column_index) This will render a column invisible. ''Coding Example'' Assuming you have a table component that is already filled with data, you could create buttons that would show hide a certain column like this: my $table = $self->application->component('myTable'); print "<input type='button' value='Hide Column 2' onclick='hide_column(\"" . $table->id() . "\", \"2\");'>"; print "<input type='button' value='Show Column 2' onclick='show_column(\"" . $table->id() . "\", \"2\");'>"; '''Note:''' The id you need to pass to the javascript function is not what you ''call'' your component with (the parameter you pass to $app->component), but rather the ''id'' ($myComponent->id() ). === TabView === Creates a tabular view. '''Example''' [[Image:Example_TabView.png]] This Tabular View was created with the following code $self->application->register_component('TabView', 'TestTabView'); my $tab_view_component = $self->application->component('TestTabView'); $tab_view_component->width(600); $tab_view_component->height(180); $tab_view_component->add_tab('Tabulator A', 'This is the content of tab a'); $tab_view_component->add_tab('Tabulator B', 'This is the content of tab b'); $tab_view_component->add_tab('Tabulator C', 'This is the content of tab c'); $tab_view_component->add_tab('Tabulator D', 'This is the content of tab d'); print $tab_view_component->output(); '''Parameters''' * '''add_tab''' (string, string) The first string passed will become the title of the tab, the second string will become the content od the tab. '''Options''' * '''width''' (int) The width of the component in pixels. * '''height''' (int) The height of the component in pixels. '''Note:''' The height of the tab header will be added to this number. * '''default''' (int) The tab initially in front. === FilterSelect === Creates a select box whose content is filtered by infix search with the string typed into an input field. The current best match will be selected. '''Example''' [[Image:Example_FilterSelect.png]] This filter select was created using the following code $self->application->register_component('FilterSelect', 'TestFilterSelect'); my $filter_select_component = $self->application->component('TestFilterSelect'); $filter_select_component->labels( [ 'Monkey', 'Donkey', 'Sponkey', 'Tronkey', 'Plonkey', 'Veronkey' ] ); $filter_select_component->values( [ 'A', 'B', 'C', 'D', 'E', 'F' ] ); $filter_select_component->size(8); $filter_select_component->width(250); $filter_select_component->name('TestFilter'); print $filter_select_component->output(); '''Parameters''' * '''labels''' (array of strings) These will become the labels of the selectable items. * '''values''' (array of strings) These will become the values of the selectable items. * '''name''' (string) The name of the select component. '''Options''' * '''size''' (int) The number of items appearing at a time. * '''width''' (int) The width of the component in pixels. === Login === Creates a login form. '''Example''' [[Image:Example_Login.png]] The login was created using the following code $self->application->register_component('Login', 'TestLogin'); my $login_component = $application->component('Login'); $login_component->small_login(1); print $login_component->output(); '''Parameters''' ''none'' '''Options''' * '''small_login''' (boolean) Setting this to true will return a smaller version of the login component. === Register === Creates a form to register a user to an application. '''Example''' [[Image:Example_Register.png]] This register component was created using the following code $self->application->register_component('Register', 'TestRegister'); my $register_component = $self->application->component('TestRegister'); print $register_component->output(); '''Parameters''' ''none'' '''Options''' ''none'' === GenomeDrawer === Draws genome related graphics. '''Example''' [[Image:ExampleGenomeDrawer.png]] This example was produced using the following code: $self->application->register_component('GenomeDrawer', 'GD1'); my $gd = $application->component('GD1'); my $line_data = [ { 'start' => 0, 'end' => 100, 'type' => 'arrow', 'title' => 'A', 'color' => 2, 'zlayer' => 1, 'description' => [ { 'title' => 'title a', 'value' => 'value a' } ] }, { 'start' => 55, 'end' => 70, 'type' => 'smallbox', 'title' => 'subA', 'color' => 1, 'zlayer' => 2 }, { 'start' => 210, 'end' => 110, 'type' => 'arrow', 'title' => 'B', 'color' => 3, 'zlayer' => 2 }, { 'start' => 250, 'end' => 390, 'type' => 'smallbox', 'title' => 'C', 'color' => 4, 'zlayer' => 2 }, { 'start' => 450, 'end' => 600, 'type' => 'bigbox', 'title' => 'D', 'color' => 5, 'zlayer' => 2 }, { 'start' => 650, 'end' => 800, 'type' => 'box', 'title' => 'E', 'color' => 6, 'zlayer' => 2 }, { 'start' => 900, 'end' => 1190, 'type' => 'ellipse', 'title' => 'F', 'color' => 7, 'zlayer' => 2 } ]; my $line_config = { 'title' => 'Line 1 which has a really long title', 'short_title' => 'Line 1', 'title_link' => 'http://www.google.de', 'basepair_offset' => 0 }; $gd->width(600); $gd->show_legend(1); $gd->window_size(1200); $gd->line_height(30); $gd->display_titles(1); $gd->add_line($line_data, $line_config); print $gd->output; '''Parameters''' * '''add_line''' (line_data, line_config) The line_data structure is an array reference of hashreferences, each hash representing one item of the line. The items have the following attributes, some of which are optional: : '''Mandatory''' :* ''start'' :: The starting base of the item :* ''end'' :: The end base of the item : '''Optional''' :* ''title'' :: The title of the item, appearing in it's popup box or above the item, if the item is an arrow and the '''display_titles''' option is set. :* ''type'' :: The shape of the item. You can see examples of each shape in the graphic above. :: Currently valid types are: ::* box ::* bigbox ::* smallbox ::* smallbox_noborder ::* ellipse ::* arrow :* ''zlayer'' :: The position of the item on the z-axis. Higher zlayers will appear over lower zlayers. :* ''color'' ::This can be either a scalar from 1 to 20, choosing the according color from the current color theme, or an array reference with three integers specifying RGB values. :* ''description'' :: This will produce a popup box, appearing upon hovering over the item. Description is an array reference of hashes. The hashes have two entries: ::* title ::* value :* ''links_list'' :: This will produce a context menu, appearing upon clicking the item. Links_list is an array reference of hashes. The hashes have two entries: ::* link ::* link_title :* onclick :: Any code passed to this will be executed upon the onclick event. The line_config (optional) is a hashreference which represents the following attributes of a line: :* ''title'' :: The title of the line (e.g. name of the organism) to be displayed in the legend. If the title is too long to fit the legend space, the short title will be displayed instead and the title will be displayed in a popup box upon hover over. :* ''short_title'' :: The short title of the line to be displayed when the title is too long to fit into the designated legend space. :* ''title_link'' :: The link to be executed when the title of a line is clicked. :* ''basepair_offset'' :: the offset of basepairs the region. Default is 0. :* ''no_middle_line'' :: This option will prevent a middle line from being drawn for this line. '''Options''' * '''width''' : The width of the graphic part of the Genome drawer in pixels. Default is 800. * '''show_legend''' : Boolean indicating whether to show line descriptions on the left border. Default is false. * '''legend_width''' : Width of the legend part of the Genome drawer in pixels. Default is 100. * '''display_titles''' : Boolean indicating whether to display gene titles over the genes (arrows). Default is false. * '''line_height''' : The height of each line in pixels. Default is 30. * '''window_size''' : the number of basepairs in the displayed region. Default is 50.000. === Hover === Creates a set of hover menus and hover tooltips. These menus and tooltips can be added to any HTML element and may be triggered by any HTML event. The example code shows you how to attach a created menu or tooltip to your element. '''Example''' $self->application->register_component('Hover', 'TestHover'); my $hover_component = $application->component('TestHover'); $hover_component->add_tooltip( 'hover_test_1', 'Hello World' ); $hover_component->add_menu( 'hover_test_2', [ 'Yahoo', 'Google' ], [ 'http://www.yahoo.de', 'http://www.google.de' ] ); print $hover_component->output(); print "<img src='./Html/info.png' id='hover_test_1' onmouseover='hover(event, \"hover_test_1\");'>"; print "<img src='./Html/info.png' id='hover_test_2' onmouseover='hover(event, \"hover_test_2\");'>"; '''Parameters''' ''none'' '''Options''' * '''add_tooltip''' (string, string, int, int) Adds a new tooltip to the tooltip container. The first string passed must be the id of the html element the tooltip should refer to. The second string can be any type of HTML. This will become the content of the tooltip. The int arguments are width (in pixels) and timeout (in milliseconds) respectively, which are optional. Default width is 150px, default timeout 8000ms. * '''add_menu''' (string, arrayref, arrayref, int, int) Adds a new hover menu to the menu container. The first string passed must be the id of the html element the menu should refer to. The second and third argument must be references to arrays. The first array must contain the strings to be displayed as the titles of the menu entries. The second array must contain the urls the menu entries should link to. The int arguments are width (in pixels) and timeout (in milliseconds) respectively, which are optional. Default width is 150px, default timeout 10000ms. === Info === Creates an information container which can be collapsed. The expanded and collapsed version can be seen in the example. The collapse/expand occurs upon clicking on the 'i'. '''Example''' [[Image:Example_Info_1.png]] [[Image:Example_Info_2.png]] This example was created using the following code: $self->application->register_component('Info', 'TestInfo'); my $info_component = $application->component('TestInfo'); $info_component->content( '...Text here...' ); print $info_component->output(); '''Parameters''' * '''content''' (string) The content of the information container. '''Options''' * '''title''' (string) The title of the information container. * '''width''' (string) The width of the information container as you would put as a css attribute (e.g. 200px or 15%). * '''default''' (boolean) If true the information container will be initially expanded, if false it will be collapsed. === HelpLink === Creates a little questionmark with a hover information. Clicking the symbol links to the wiki. '''Example''' [[Image:Example_HelpLink.png]] This example was created using the following code: $self->application->register_component('HelpLink', 'test_help_component'); my $help_component = $application->component('test_help_component'); $help_component->page('myWikiPage'); $help_component->title('myTitle'); $help_component->text('Short informative text.'); print $help_component->output(); '''Parameters''' * '''text''' (string) The content of the help hover. * '''title''' (string) The title of the help hover. '''Options''' * '''page''' (string) The wiki page the help link will link to. Default is the value of title. * '''wiki''' (string) The base url of the wiki to link to. Default is 'http://www.theseed.org/wiki/' * '''hover_width''' (int) The width of the hover info box in pixels. Default is 150px. === PieChart === Creates a pie chart. '''Example''' [[Image:Example_PieChart.png]] This example was created using the following code: $self->application->register_component('PieChart', 'test_pie'); my $pie = $application->component('test_pie'); $pie->data( [ 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10 ] ); print $pie->output(); '''Parameters''' * '''data''' (array of int) The array of values to be displayed. '''Options''' * '''size''' (int) The size of the chart in pixels. Default is 400. === Ajax === Component for Ajax support. This will allow you to reload parts of your page, without having to reload the entire page. You can write any function in your WebPage module and call it via this mechanism. You will have access to the application object in that function. This means you have access to session information as well as any components which were registered in the original calling of your page. '''Example''' $self->application->register_component('Ajax', 'test_ajax'); print $application->component('test_ajax')->output(); print "&lt;div id='ajax_target'>&lt;/div>"; my $no_loading_image = 0; print qq~<form id="ajax_source" action="javascript:execute_ajax('myFunction', 'ajax_target', 'ajax_source', 'loading_text', $no_loading_image);">~; print "<input type='text' name='test_text' value='Hello World'><input type='submit'>"; print "</form>"; use URI::Escape; my $text = uri_escape("Hello World"); print qq~<a href="javascript:execute_ajax('myFunction', 'ajax_target', 'test_text=~ . $text . qq~');">click me</a>~; sub myFunction { my ($self) = @_; my $cgi = $self->application->cgi(); return $cgi->param('test_text'); } '''Parameters''' The actual parameters are passed to the '''execute_ajax''' javascript. :* '''function''' :: The name of the function in MyPage.pm which will return the content to be displayed in the target div. :* '''target''' :: The id of the div the result of the called function should appear in '''Options''' The options are passed to the '''execute_ajax''' javascript. :* '''source''' :: This can be either the id of a form whose content will be passed to the called function in MyPage.pm or a uri-encoded string of key-value pairs as shown in the example. :* '''loading_text''' :: This text will be displayed next to the loading image, displayed until the perl function returns the content. Default is: 'Loading...'. :* '''no_loading_text''' :: If set to 1, no loading text will be displayed. Default is 0. === Tree === Component to create treeviews of various kinds. Right now, only a very simple version is supported, but it is currently being expanded. '''Example''' [[Image:Example_Tree.png]] This example was created using the following code: $self->application->register_component('Tree', 'Testtree'); my $tree = $application->component('Testtree'); my $lvl1 = ['Grandfather A','Grandfather B','Grandfather C','Grandfather D']; foreach my $l1 (@$lvl1) { my $lvl2 = ['Father A','Father B']; my $node = $tree->add_node( { 'label' => $l1 } ); foreach my $l2 (@$lvl2) { my $lvl3 = ['Child A', 'Child B', 'Child C']; my $child = $node->add_child( { 'label' => $l2 } ); foreach my $l3 (@$lvl3) { $child->add_child( { 'label' => $l3 } ); } } } print $tree->output(); '''Parameters''' * '''add_node''' ( { 'label' => $label, 'expanded' => $expanded } ) Adds a node to the tree with the given label. The optional 'expanded' attribute is a boolean indicating whether the node is initially expanded or not. Default is false. '''Options''' * '''node->add_child''' ( { 'label' => $label, 'expanded' => $expanded } ) Adds a child to a node. == Supporting Components == === WebGD === The WebGD Component is used to produce Internet Explorer safe images. Since we want to support IE and IE does not support inline images, you should use WebGD anytime you create a component that creates inline images. WebGD functions in the same way that '''GD::Image''' does. It has one additional method '''image_src''' which returns you the src-part of the html image tag to display your image. '''Usage''' use WebGD; my $image = WebGD::new($width, $height); $image->line($x1, $y1, $x2, $y2, $color); ... draw your image ... print "<img src='" . $image->image_src() . "'>"; This will detect whether the client is IE or another browser. IE will cause it to create a temporary file and link it, all other browsers support inline images, so WebGD will use base64 encoding to produce an inline image. '''Caution''' Make sure that the variables ''$temp_url'' and ''$temp'' are set correctly in you FIG_Config.pm, as those paths will be used by WebGD. 8a50263072c72360f288a85c9a1ef723caa8d8e9 0 1443 1746 2007-10-05T20:06:57Z TobiasPaczian 17 wikitext text/x-wiki == Introduction == The PPO allows you to use the object orientation of perl, with persistent store of the object in mySQL. The objects you create with the PPO are a direct representation of the database, meaning that changes to an object will immediately be stored. On this page, you will get a detailed example of the usage of the PPO. For a short overview, please refer to [[Persistent Perl Objects]]. This guide is split into six parts: * setup of PPO * creation of an object schema * generation of the modules * using PPO in your scripts * customize access to objects * troubleshooting == Setup == For the course of this example, let us assume we want to create a little application that handles the management of users. We will call this application UserManagement. The programmer doing this will be called Joe User, his login is juser. Since we are experimenting with new stuff, we want to do this in our sandbox. If your environment does not automatically do this, you must first source the config file, depending on your shell, either config.sh or config.csh. cd ~/FIGdisk/config/ source fig-user-env.sh or cd ~/FIGdisk/config/ source fig-user-env.csh The source code of PPO resides in CVS, so we now switch to the main source directory and check out PPO. Note that you only need the -d option, if you have not automatically done so in your environment. You must put your login in the string where it says juser. cd ~/FIGdisk/dist/releases/current/ cvs -d :ext:juser@biocvs.mcs.anl.gov:/disks/cvs/bio checkout PPO Something like the following should happen: cvs checkout: Updating PPO U PPO/.cvsignore U PPO/DBMaster.pm U PPO/DBObject.pm U PPO/DBObjectCache.pm U PPO/DBSQLArray.pm U PPO/Makefile U PPO/PPOBackend.pm U PPO/PPOGenerator.pm U PPO/generate.pl cvs checkout: Updating PPO/PPOBackend U PPO/PPOBackend/MySQL.pm U PPO/PPOBackend/SQLite.pm The PPOGenerator.pm contains the functionality to create the neccesary files from the object schema you create, so you can access your objects. The generate.pl script is called to generate the perl modules and setup the databases. The DBMaster.pm, DBObject.pm, DBSQLArray.pm and DBObjectCache.pm contain the core functionality of PPO. The PPOBackend.pm module and it's subdirectory provide the PPO with access to different database technologies (currently MySQL and SQLite). == Object Schema == Before we can create an object schema for our little application, we create a directory for it. mkdir ~/FIGdisk/dist/releases/current/UserManagement Within this directory we create the schema file with the text editor of your choice. In our example, the file will be called '''UserManagement.xml'''. To start off, we tell the xml, that we are using xml. <?xml version="1.0" encoding="UTF-8"?> Then we make an opening and closing tag for our project. PPO supports the integration of multiple schemata into one superspace. Our user management for example, might be part of a larger application. Other schemata might be referencing to objects in our UserManagement space. This larger scale concept is called '''Superspace'''. Since we have no large scale concept yet, we leave the superspace blank. <?xml version="1.0" encoding="UTF-8"?> <project_space label="UserManagement" superspace=""> </project_space> Now we are ready to create the first object. Every object needs a name and since we want to create a user management, we need a User. The user object should also have some attributes, e.g. firstName, lastName, login and password. Each user must have a login, so we make that attribute mandatory to make sure a user object cannot be created without a login. <?xml version="1.0" encoding="UTF-8"?> <project_space label="UserManagement" superspace=""> <object label="User"> <scalar label="firstName" type="CHAR(250)" /> <scalar label="lastName" type="CHAR(250)" /> <scalar label="login" type="CHAR(250)" mandatory="1" /> <scalar label="password" type="CHAR(250)" /> </object> </project_space> Every attribute must have a type. In case of scalar attributes, this can be any valid mySQL data type. You can find information about mySQL data types [http://dev.mysql.com/doc/refman/5.1/en/data-types.html here]. When choosing names for Objects and their attributes, bear in mind that you may not use words reserved by mySQL. A current list of these words can be found [http://dev.mysql.com/doc/refman/5.1/en/reserved-words.html here]. Now we also want to make sure no two users get the same login. To achieve this we need to create an index. To create an index, include all attributes that should be contained in the index. If we assume for example that every user is unique if you take a combination of first and last name, include both firstName and lastName inside the index tag. Since there might to two people with the same first and last name, we rather use the login as the index. This will make sure no two users will get the same login. Also we want to introduce a default value. We will default the password for every user to 'secret'. Of course you know that in a real application you would a) encrypt the password and b) never set a default password. <?xml version="1.0" encoding="UTF-8"?> <project_space label="UserManagement" superspace=""> <object label="User"> <scalar label="firstName" type="CHAR(250)" /> <scalar label="lastName" type="CHAR(250)" /> <scalar label="login" type="CHAR(250)" mandatory="1" /> <scalar label="password" type="CHAR(250)" default="secret" /> <index> <attribute label="login" /> </index> </object> </project_space> Multiple indices require multiple index tags. However, it is unlikely you will need more than one index for one object type. To make things a little more complex, we would like to store the organization of every user. Since multiple users are likely to share the same organization, we want to create a new object type Organization to maintain normalization. The User object will then receive an attribute which is a reference to an Organization object. In this case, the type of the attribute is the name of the referenced object type. To make sure no two organizations have the same name, we index the name of the organization. This will also allow us to init an Organization object via its name. <?xml version="1.0" encoding="UTF-8"?> <project_space label="UserManagement" superspace=""> <object label="User"> <scalar label="firstName" type="CHAR(250)" /> <scalar label="lastName" type="CHAR(250)" /> <scalar label="login" type="CHAR(250)" mandatory="1" /> <scalar label="password" type="CHAR(250)" /> <index> <attribute label="login" /> </index> <object label="organisation" type="Organisation" /> </object> <object label="Organisation"> <scalar label="name" type="CHAR(255)" mandatory="1" /> <scalar label="abbreviation" type="CHAR(255)" /> <scalar label="url" type="CHAR(255)" /> <index> <attribute label="name" /> </index> </object> </project_space> The last thing we do is to introduce an array attribute. We want every user to have a list of rights, so we can differentiate which user may do what in our little application. <?xml version="1.0" encoding="UTF-8"?> <project_space label="UserManagement" superspace=""> <object label="User"> <scalar label="firstName" type="CHAR(250)" /> <scalar label="lastName" type="CHAR(250)" /> <scalar label="login" type="CHAR(250)" mandatory="1" /> <scalar label="password" type="CHAR(250)" /> <index> <attribute label="login" /> </index> <object label="organisation" type="Organisation" /> <array> <scalar label="rights" type="CHAR(255)" /> </array> </object> <object label="Organisation"> <scalar label="name" type="CHAR(255)" mandatory="1" /> <scalar label="abbreviation" type="CHAR(255)" /> <scalar label="url" type="CHAR(255)" /> <index> <attribute label="name" /> </index> </object> If you want to have multiple array attributes within one object, put them all in the same array tag. You may also have array attributes which are references to objects. Be careful though, usually object array attributes can be easily substituted by refining the schema and they are computationally very expensive. == Module Generation == Now that the object schema is complete, we can generate the modules with the generate script. The script is located in the PPO directory and must be called with a set of parameters. perl ~/FIGdisk/dist/releases/current/PPO/generate -f schemafilename -t targetdirectory -d databasename In our case the schemafilename will be '''UserManagement.xml''', the target directory will be '''~/FIGdisk/dist/releases/current/UserManagement/''' and the database name will be '''UserManagement'''. This will produce the following files: UserManagement.pm UserManagement.sql UserManagement/ObjectBase.pm UserManagement/User.pm UserManagement/Organization.pm Now you can setup the mySQL database by just calling mysql -u root < UserManagement.sql This will generate all necessary tables for you. You are now ready to use the object schema you created. However, the modules User.pm and Organization.pm allow you to customize all calls to your objects. You can read more about this in the '''Customize''' section. == Example Script == Now we will create a little script called user_management.pl which will use our freshly created object schema. To be nice we use strict and warnings and for the PPO we need to use DBMaster. Then the first thing we do is get a DBMaster object. This is our general access mechanism to all features of PPO. The only argument the DBMaster needs is the database name. use strict; use warnings; use DBMaster; my $dbmaster = DBMaster->new('UserManagement'); Using the DBMaster object, we can now create a new User object. We pass all attributes to the creator using a hash structure. We can omit any attributes we wish, except for the madatory attribute login. Also, we created and index on login, so we may not create objects with a value for login already posessed by another object. To ensure this does not happen, we try to init a User object with the login we create. my $login = 'juser'; my $firstName = 'Joe'; my $lastName = 'User'; my $password = 'secret'; my $user; unless ( $user = $dbmaster->User->init( { login => $login } ) ) { $user = $dbmaster->User->create( { firstName => $firstName, lastName => $lastName, login => $login, password => $password } ); } Now the new_user variable will contain a reference to the newly created object. If the object creation failed, the variable will be undef. Now let's create another object, this time of the type Organization. my $org_name = 'Acme Industries'; my $org_abbrev = 'AI'; my $org_url = 'www.acme.com'; unless ( $dbmaster->Organization->init( { name => $org_name } ) ) { my $new_organization = $dbmaster->Organization->create( { name => $org_name, abbreviation => $org_abbrev, url => $org_url } ); } Joe User is part of Acme Industries, so let us add this information to his user object. $new_user->organization( $new_organization ); That was easy. Now let's examine if it all worked correctly and print the information in the user object. print "User Summary\n"; print "First Name : " . $new_user->firstName() . "\n"; print "Last Name : " . $new_user->lastName() . "\n"; print "Login : " . $new_user->login() . "\n"; print "Password : " . $new_user->password() . "\n"; print "Organization : " . $new_user->organization->name() . "\n"; That will print out the data stored in our newly created objects. Let us imagine we have created a number of users and we want to get them all. my $all_users = $dbmaster->User->get_objects( {} ); foreach my $user (@$all_users) { print $user->firstName . " " . $user->lastName . "\n"; } Now imagine that Acme Industries went bankrupt and all their users should be deleted from our database. my $acme = $dbmaster->Organization->init( { name => 'Acme Industries' } ); my $acme_users = $dbmaster->User->get_objects( { organization => $acme } ); foreach my $acme_user ( @$acme_users ) { $acme_user->delete(); } This concludes the PPO example. The next chapter talks about customization of your object modules. == Customize == The PPO allows you to customize the access methods for your objects, you can even create new methods. Let's pick up the example from above about the UserManagement. Imagine you always want to retrieve the list of users, ordered by name. The normal retrieval method '''get_objects''' would retrieve the data in the order of creation by default. The following example shows how this could be handled by overwriting the get_objects method. UserManagement/User.pm package WebApplicationServer::User; use strict; use warnings; 1; # this class is a stub, this file will not be automatically regenerated # all work in this module will be saved sub get_objects { # get the parameters given to the function my ($self, $values) = @_; # call the original method my $objects = $self->SUPER::get_objects($values); # do the sorting my @sorted_objects = sort { $a->lastName cmp $b->lastName || $a->firstName cmp $b->firstName } @$objects; # return the result return \@sorted_objects; } == Troubleshooting == '''Problem:''' I call generate.pl and it tells me 'cannot open mysql_reserved'. '''Solution:''' You must call generate.pl from the PPO directory, since mysql_reserved is expected to be in the directory you call generate.pl from. 922f6ea32e2b1838938cf875c8b1bc2c3a9d4338 0 1444 1747 2007-10-05T20:07:18Z TobiasPaczian 17 wikitext text/x-wiki On this page you will find the definition of the XML used to generate a PPO object schema. To clarify the descriptions below note the following. The '''XML schema''' is the representation of an '''Object schema'''. The term '''attribute''' may be used in both contexts, but refers to different things. == Document == A document must start with the following tag: <?xml version="1.0" encoding="UTF-8"?> '''Note:''' All chosen names within an XML-definition '''may not''' be from a list of reserved words (across all supported database backends). A good starting point what to avoid is the list of [http://dev.mysql.com/doc/refman/5.1/en/reserved-words.html MySQL reserved words]. == XML Tags == === project === Each project is encapsulated within a single database. Multiple projects may be hosted on one database-server. Projects that are to interact with each other '''must''' be hosted on the same database-server. The project tag surrounds the description of all objects within this project. The name of the project is reflected in the '''label''' attribute of the project tag. This will also be the name of the directory the generated perl-modules will reside. Projects may contain object elements. <project label="MyProjectName"> ... </project> === object === Objects must reside inside of projects. They represent the types of data-objects which can be stored, retrieved and manipulated using the PPO. The object tag must be closed. The object must be named using the '''label''' attribute. This is the name the object can be accessed through. Objects may contain elements, representing their object-attributes and indices. <object label="MyObjectName"> ... </object> === scalar === The scalar element represents an attribute of an object and may only appear within an object element. The label attribute of this element will be the name of the object attribute. The type attribute can be any of the following data types (the exact size and implementation of each data type depends on the backend): * BOOLEAN: true or false * INTEGER: signed integer value * FLOAT: signed floating-point number * TIMESTAMP: timestamp as number of seconds since the epoch * CHAR(n): field of n characters * TEXT: text field (eg. 64kb) * TEXT LONG: large text field (eg. 4GB) * BLOB: data blob, stored as input * BLOB LONG: large data blob <scalar label="myAttributeName" type="INTEGER" /> === object_ref === The object_ref element represents a reference to an object which is an attribute of the surrounding object. The label attribute of this element will be the name of the object attribute. The type attribute can be any object name; it may refer to objects within the same project or to object in other projects. If the referenced object is not stored in the same database, the type attribute must be preceeded by ''' 'MyProjectName::' '''. <object_ref label="myObjectAttributeName" type="ObjectTypeWithinThisProject" /> or <object_ref label="myObjectAttributeName" type="MyProjectName::ObjectTypeWithinOtherProject" /> === array === The array element represents an attribute of the surrounding object which is an array. Arrays must consist exactly one instance of either a scalar or an object_ref. <array> <scalar label="myObjectAttributeName" type="INTEGER" /> </array> or <array> <object_ref label="myObjectAttributeName" type="MyObjectType" /> </array> === index === The index element defines a mySQL index for this object for faster accession. Any combination of the scalar attributes of an object may be indexed, however, you may not index on arrays or object references. Each attribute to be part of the index must be listed via an attribute element. The attribute elements label attribute must be the name of the object attribute to be part of the index. You may create any number of indices. <index> <attribute label="myObjectAttributeNameA"> <attribute label="myObjectAttributeNameB"> ... </index> === unique_index === The unique_index element defines a set of attributes for an object which in combination must be unique. Any combination of the scalar attributes of an object may be indexed, however, you may not index on arrays or object references. Each attribute to be part of the index must be listed via an attribute element. The attribute elements label attribute must be the name of the object attribute to be part of the index. You may create any number of indices. <unique_index> <attribute label="myObjectAttributeNameA"> <attribute label="myObjectAttributeNameB"> ... </unique_index> Creating a unique index will cause an '''init''' method to be created for this combination of attributes, allowing you access to instances of this object. my $object = $dbmaster->myObject->init( { attribute1 => 'value1', attribute2 => 'value2' } ); b0c5077edb7e3a86146646d8ed15ef2a01dbc9d2 0 1445 1748 2007-10-05T20:09:22Z TobiasPaczian 17 wikitext text/x-wiki The Persistent Perl Objects (PPO) provide a functionality to store perl objects persistently in a mySQL database. == Overview == The PPO allows you to create an object schema in XML, which will be used to generate: * an SQL file to create the underlying database * a set of perl modules to create, read, update and delete objects * a set of perl stub modules to create custom access methods for the objects if desired On this page you will get a short introduction on how to use the PPO. A more detailed example can be found at [[PPO Example]]. You can find the definition of the XML at [[PPO XML Definition]]. == Source == The PPO module is checked into CVS. If you wish to use it, check it out to your cvs working directory and make sure it is in your path so the perl interpreter can find it. Something like the following should happen: username@biologin-1:~/cvs$ cvs co PPO Enter passphrase for key '/home/username/.ssh/id_rsa': cvs checkout: Updating PPO U PPO/.cvsignore U PPO/DBMaster.pm U PPO/DBObject.pm U PPO/DBObjectCache.pm U PPO/DBSQLArray.pm U PPO/Makefile U PPO/PPOBackend.pm U PPO/PPOGenerator.pm U PPO/generate.pl cvs checkout: Updating PPO/PPOBackend U PPO/PPOBackend/MySQL.pm U PPO/PPOBackend/SQLite.pm == Usage == First, create a directory to store your project files. Within this directory, create an XML file to describe your object schema. The XML must have the following format: <?xml version="1.0" encoding="UTF-8"?> <project_space label="ProjectName1"> <object label="ObjectName1"> <scalar label="attributeName1" type="int" mandatory="1" /> <scalar label="attributeName2" type="CHAR(25)" /> <scalar label="attributeName3" type="text" default="-" /> <object_ref label="attributeName6" type="ProjectName1::ObjectName7" /> <array> <object_ref label="attributeName4" type="ProjectName2::ObjectName2" /> </array> <array> <scalar label="attributeName5" type="boolean" /> </array> <unique_index> <attribute label="attributeName1" /> <attribute label="attributeName2" /> </unique_index> </object> </project_space> After creating the schema file, you can call the generate script from the PPO to # create the perl modules and # create the PPO database on your database system. generate.pl -xml xml_file -perl_target target_dir/ This will create a perl modules for your schema and a subdirectory with the neccessary ObjectBase.pm file which contains the access methods for your objects. Within this directory, you will also find a separate perl module for every object type in your schema. These files are stubs that allow you to customize the access methods to the according objects. Note: the trailing '/' is important for the -perl_target parameter! generate.pl -xml xml_file -backend db_backend -database db_name e.g.: generate.pl -xml xml_file -backend MySQL -database my_db_name -user root Run this command to create database on your database host. For this to work best, you have to be on the machine the database server runs on (in our case that's biofiler). The setup of your schema is now complete. The following example will demonstrate how to use it in your code. # include the Database Master Module use DBMaster; # initialize a DBMaster object my $dbmaster = DBMaster->new(-database => 'my_db_name'); # create an object, passing attributes as a hash my $new_object = $dbmaster->MyObject->create( { attribute1 => 'value1', attribute2 => 'value2' } ); # it's a good idea to check what you got back unless (ref $new_object) { # substitute with a more appropriate reaction die "Unable to create object."; } # change an attribute value $new_object->attribute1( 'new_value' ); # retrieve an attribute value my $value = $new_object->attribute1(); # get a single object, using an indexed attribute my $new_object2 = $dbmaster->MyObject->init( { key_attribute1 => 'value1' } ); # get all objects that match the passed attribute values my $object_list_array_reference = $dbmaster->MyObject->get_objects( { attribute1 => 'value1' } ); foreach (@$object_list_array_reference) { # do something with each element of that array } # delete an object (and remove it from the database) $new_object->delete(); 7dff95c2c3658ad46b57082fd197a4e8c8142673 8 1090 1752 1707 2007-12-09T00:47:31Z FolkerMeyer 2 wikitext text/x-wiki * Navigation ** Home_of_the_SEED|Home of the SEED ** Annotating_1000_genomes|Manifesto ** SEED_People| SEED People ** Contact| Contact * SEEDs ** http://seed-viewer.theseed.org/|SEED-Viewer ** http://theseed.uchicago.edu/FIG/index.cgi|Trial-SEED * Applications ** http://rast.nmpdr.org/|RAST Annotation Server ** http://metagenomics.nmpdr.org/|Metagenomics RAST Server * Documentation ** RAST_Tutorial|RAST Server Tutorial ** MG_RAST_Tutorial|MG-RAST Tutorial ** SEED_Viewer_Tutorial|SEED Viewer Tutorial ** Video_Tutorials|Video Tutorials * Miscellaneous ** DownloadPage|Download Page ** Glossary|FAQ Frequently Asked Questions ** Glossary|Glossary ** SOPs|SOPs ** SpecialPurposeDBs|Special Purpose DBs 114ac7c6a7aa89f9ccc974a5d9b0334870177163 0 1367 1753 1702 2007-12-09T00:50:23Z FolkerMeyer 2 wikitext text/x-wiki === Annotators SEED === The master copy for all data in the SEED environment. Users can not access this password protected site. All annotations are made available via the [[#SEED-Viewer| SEED-Viewer]] and the [[#Trial-SEED|Trial-SEED]]. === Annotation === please see [[#Assigning_a_gene_function_and_annotation| Assigning a gene function and annotation]] === Assigning a gene function and annotation === Annotators assign gene functions to genes, and we call this process annotation. In most contexts, people use the term annotation to refer to assignments of function to the genes within a single organism. We certainly use the term in this sense, but we also use it to describe the process of assigning functions to corresponding genes from numerous genomes. Our basic approach to annotation is to ask our annotators to annotate the genes included in a [[#subsystem|Subsystem]] (e.g., glycolysis) across all genomes. This process of annotation of the genes within a subsystem across a set of genomes, rather than annotation of genes within a single genome, allows our annotators to focus on a constrained set of functional roles and attempt to accurately identify exactly what variant, if any, of a subsystem exists in each of the genomes. We use the term annotation to refer to assigning functions to genes (either within a single organism or to a constrained set of gene/protein families across a set of organisms). This activity certainly is closely related to the construction of subsystems and protein families (which we call FIGfams), but we will describe those activities elsewhere. === Assignment === please see [[#Assigning_a_gene_function_and_annotation| Assigning a gene function and annotation]] === Bidirectional Best Hit (BBH) === The paper [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=EBI&pubmedid=10077608 The use of gene clusters to infer functional coupling] defines a Bidirectional Best Hit or BBH as follows: <blockquote> Given two genes Xa and Xb from two genomes Ga and Gb, Xa and Xb are called a “bidirectional best hit (BBH)” if and only if recognizable similarity exists between them (in our case, we required fasta3 scores lower than 1.0 × 10−5), there is no gene Zb in Gb that is more similar than Xb is to Xa, and there is no gene Za in Ga that is more similar than Xa is to Xb. Genes (Xa, Ya) from Ga and (Xb, Yb) from Gb form a “pair of close bidirectional best hits (PCBBH)” if and only if Xa and Ya are close, Xb and Yb are close, Xa and Xb are a BBH, and Ya and Yb are a BBH. </blockquote> === Clearinghouse === please see [[#SubsystemClearinghouse|Subsystem Clearinghouse]] ===Feature=== A feature is a defined region in the DNA. A PEG is the most prevalent feature type in the SEED. Some other feature types include RNA, prophage and pathogenicity islands. The format for a feature ID is fig|genome_id.feature_abbreviation.feature_number (ie fig|83333.1.peg.100 ). === FIGfam === FIGfams are protein families generated by the Fellowship for Interpretation of Genomes (FIG). These families are based on the collection of subsystems, as well as correspondences between genes in closely related strains (we describe the construction of FIGfams in a separate SOP). The important properties of these families are as follows: # Two PEGs which both occur within a single FIGfam are believed to have the same function. # There is a decision procedure associated with the family which can be invoked to determine whether or not a gene can be “safely” assigned the function associated with the family. === Functional role === The concept of functional role is both basic and primitive in the sense that we will not pretend to offer a precise definition. It corresponds roughly to a single logical role that a gene or gene product may play in the operation of a cell. === Gene function === The function of a protein-encoding gene (PEG) is the functional role played by the product of the gene or an expression describing a set of roles played by the encoded protein. The operators used to construct expressions and the meanings associated with the operators are described in http://www.nmpdr.org/FIG/Html/SEED_functions.html Genes other than PEGs can also be assigned functions (e.g., SSU rRNA). However, in most cases the functions assigned to genes other than PEGs tend not to be problematic. === Linking to the SEED === We support linking to the SEED using a generic mechanism: Base URL: http://www.theseed.org/linkin.cgi? {| |+ Supported SEED Identifiers for external use ! Entity type !! key !! identifier !! Example |- | Genome || genome || fig<nowiki>|</nowiki>83331.1 || [[http://www.theseed.org/linkin.cgi?genome=fig|83333.1 http://www.theseed.org/linkin.cgi?genome=fig&#124;83333.1]] |- | PEG || id || fig<nowiki>|</nowiki>83331.peg.123 || [[http://www.theseed.org/linkin.cgi?id=fig|83333.1.peg.123 http://www.theseed.org/linkin.cgi?id=fig&#124;83333.1.peg.123]] |- | RNA feature || id || fig<nowiki>|</nowiki>83331.rna.1 || [[http://www.theseed.org/linkin.cgi?id=fig|83333.1.rna.1 http://www.theseed.org/linkin.cgi?id=fig&#124;83333.1.rna.1]] |- |} SEED identifiers contain the NCBI taxonomy ID, thus if the taxonomy ID changes, we need to update our internal data accordingly. To provide stable external identifiers, we keep a list of IDs that have changed and display warning message informing the user of the change and provide a link to the new version of the data requested. === Metabolic Reconstruction === When we use the term metabolic reconstruction of a given genome we will simply mean the set of populated subsystems that contain the genome, the PEGs (and their assigned functions) that are connected to functional roles in these populated subsystems, and the specific variant code associated with the genome in each of the populated subsystems. === NMPDR pathogen genome === The NMPDR is responsible for five classes of genomes: # Campylobacter jejuni # Listeria monocytogenes # Staphylococcus aureus # Streptococcus pneumoniae and Streptococcus pyogenes # Pathogenic Vibrio === Pair of Close Homologs (PCH) === The paper [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=EBI&pubmedid=10077608 The use of gene clusters to infer functional coupling] defines a Pair of Close Homologs as follows: <blockquote> We can also define the concept of “pairs of close homologs” (PCHs) as follows: genes (X′a, Y′a) from Ga and (X′b, Y′b) from Gb form a PCH if and only if X′a and Y′a are close, X′b and Y′b are close, X′a and X′b are recognizably similar, and Y′a and Y′b are recognizably similar. Here, we will consider two genes to be recognizably similar if their gene products produce fasta3 scores lower than 1.0 × 10−5. We use a scoring scheme analogous to the one described for PCBBHs to evaluate the connections between PCHs, except that if Ga and Gb are the same genome, we assign an arbitrary “same-genome score” (“same-genome” pairs cannot occur for PCBBHs by definition, but for PCHs they are possible). Unlike PCBBHs from two very close genomes for which contiguity is completely uninformative in the vast majority of cases, PCHs allow recognition of gene clusters that play similar (but usually not identical) roles (such as two transport cassettes containing pairs of homologs) in the same or similar organisms. The arbitrary “same-genome score” should, we believe, have a value that is high enough to rank such instances as significant. </blockquote> === PEG === A Protein Encoding Gene (PEG) is equivalent to a CDS (Coding Sequence). === Populated Subsystem === please see [[#Subsystem|Subsystem]] === SEED-Viewer === The SEED Viewer is a web-based application that allows browsing of SEED data structures. We use the SEED-Viewer to provide a public read-only version of the latest SEED data at: http://seed-viewer.theseed.org '''Please note''': The data is updated automatically every 24 hours. When citing or linking to the SEED please use this version. === Subsystem === A subsystem is a set of functional roles that an annotator has decided should be thought of as related. Frequently, subsystems represent the collection of [[#Functional_role|functional roles]] that make up a metabolic pathway, a complex (e.g., the ribosome), or a class of proteins (e.g., two-component signal-transduction proteins within Staphylococcus aureus). A '''populated subsystem''' is a subsystem with an attached spreadsheet. The rows of the spreadsheet represent genomes and the columns represent the functional roles of the spreadsheet. Each cell contains the identifiers of genes from the corresponding genome the implement the specific functional role. That is, a populated subsystem specifies which genes implement instances of the subsystem in each of the genomes. The rows of a populated genome are assigned '''variant codes''' which describe which of a set of possible variants of the subsystem exist within each genome (special codes expressing a total absence of the subsystem or remaining uncertainty exist). Construction of a large set of curated populated subsystems is at the center of the NMPDR and SEED annotation efforts. === Subsystem Clearing House === Since annotators can work on any machine (including the public SEED) the way to propagate subsystems is via http://clearinghouse.theseed.org/clearinghouse_browser.cgi? === Trial-SEED === A public, read-write copy of the SEED is made available on http://theseed.uchicago.edu/FIG/index.cgi '''Please note''': The data on this server is updated in irregular intervals. Users should not assume that annotations made on this system will persist. Please publish your annotations to the [[#Subsystem_clearing_house|Subsystem Clearing house]]. === Variant Code=== please see [[#Subsystem|Subsystem]] 827fc3cf4eab82013e896b9db8a4d0853ee37586 1754 1753 2007-12-09T00:54:04Z FolkerMeyer 2 wikitext text/x-wiki === Annotators SEED === The master copy for all data in the SEED environment. Users can not access this password protected site. All annotations are made available via the [[#SEED-Viewer| SEED-Viewer]] and the [[#Trial-SEED|Trial-SEED]]. === Annotation === please see [[#Assigning_a_gene_function_and_annotation| Assigning a gene function and annotation]] === Assigning a gene function and annotation === Annotators assign gene functions to genes, and we call this process annotation. In most contexts, people use the term annotation to refer to assignments of function to the genes within a single organism. We certainly use the term in this sense, but we also use it to describe the process of assigning functions to corresponding genes from numerous genomes. Our basic approach to annotation is to ask our annotators to annotate the genes included in a [[#subsystem|Subsystem]] (e.g., glycolysis) across all genomes. This process of annotation of the genes within a subsystem across a set of genomes, rather than annotation of genes within a single genome, allows our annotators to focus on a constrained set of functional roles and attempt to accurately identify exactly what variant, if any, of a subsystem exists in each of the genomes. We use the term annotation to refer to assigning functions to genes (either within a single organism or to a constrained set of gene/protein families across a set of organisms). This activity certainly is closely related to the construction of subsystems and protein families (which we call FIGfams), but we will describe those activities elsewhere. === Assignment === please see [[#Assigning_a_gene_function_and_annotation| Assigning a gene function and annotation]] === Bidirectional Best Hit (BBH) === The paper [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=EBI&pubmedid=10077608 The use of gene clusters to infer functional coupling] defines a Bidirectional Best Hit or BBH as follows: <blockquote> Given two genes Xa and Xb from two genomes Ga and Gb, Xa and Xb are called a “bidirectional best hit (BBH)” if and only if recognizable similarity exists between them (in our case, we required fasta3 scores lower than 1.0 × 10−5), there is no gene Zb in Gb that is more similar than Xb is to Xa, and there is no gene Za in Ga that is more similar than Xa is to Xb. Genes (Xa, Ya) from Ga and (Xb, Yb) from Gb form a “pair of close bidirectional best hits (PCBBH)” if and only if Xa and Ya are close, Xb and Yb are close, Xa and Xb are a BBH, and Ya and Yb are a BBH. </blockquote> === Clearinghouse === please see [[#SubsystemClearinghouse|Subsystem Clearinghouse]] ===Feature=== A feature is a defined region in the DNA. A PEG is the most prevalent feature type in the SEED. Some other feature types include RNA, prophage and pathogenicity islands. The format for a feature ID is fig|genome_id.feature_abbreviation.feature_number (ie fig|83333.1.peg.100 ). === FIGfam === FIGfams are protein families generated by the Fellowship for Interpretation of Genomes (FIG). These families are based on the collection of subsystems, as well as correspondences between genes in closely related strains (we describe the construction of FIGfams in a separate SOP). The important properties of these families are as follows: # Two PEGs which both occur within a single FIGfam are believed to have the same function. # There is a decision procedure associated with the family which can be invoked to determine whether or not a gene can be “safely” assigned the function associated with the family. === FIG Identifier / FIG-IDs === We provide identifiers for genome sequences and features in the following form: {| |+ Supported SEED Identifiers for external use ! Entity type !! key !! identifier |- | Genome || genome || fig<nowiki>|</nowiki>83331.1 |- | PEG || id || fig<nowiki>|</nowiki>83331.peg.123 |- | RNA feature || id || fig<nowiki>|</nowiki>83331.rna.1 |- |} === Functional role === The concept of functional role is both basic and primitive in the sense that we will not pretend to offer a precise definition. It corresponds roughly to a single logical role that a gene or gene product may play in the operation of a cell. === Gene function === The function of a protein-encoding gene (PEG) is the functional role played by the product of the gene or an expression describing a set of roles played by the encoded protein. The operators used to construct expressions and the meanings associated with the operators are described in http://www.nmpdr.org/FIG/Html/SEED_functions.html Genes other than PEGs can also be assigned functions (e.g., SSU rRNA). However, in most cases the functions assigned to genes other than PEGs tend not to be problematic. === Linking to the SEED === We support linking to the SEED using a generic mechanism: Base URL: http://www.theseed.org/linkin.cgi? {| |+ Supported SEED Identifiers for external use ! Entity type !! key !! identifier !! Example |- | Genome || genome || fig<nowiki>|</nowiki>83331.1 || [[http://www.theseed.org/linkin.cgi?genome=fig|83333.1 http://www.theseed.org/linkin.cgi?genome=fig&#124;83333.1]] |- | PEG || id || fig<nowiki>|</nowiki>83331.peg.123 || [[http://www.theseed.org/linkin.cgi?id=fig|83333.1.peg.123 http://www.theseed.org/linkin.cgi?id=fig&#124;83333.1.peg.123]] |- | RNA feature || id || fig<nowiki>|</nowiki>83331.rna.1 || [[http://www.theseed.org/linkin.cgi?id=fig|83333.1.rna.1 http://www.theseed.org/linkin.cgi?id=fig&#124;83333.1.rna.1]] |- |} SEED identifiers contain the NCBI taxonomy ID, thus if the taxonomy ID changes, we need to update our internal data accordingly. To provide stable external identifiers, we keep a list of IDs that have changed and display warning message informing the user of the change and provide a link to the new version of the data requested. === Metabolic Reconstruction === When we use the term metabolic reconstruction of a given genome we will simply mean the set of populated subsystems that contain the genome, the PEGs (and their assigned functions) that are connected to functional roles in these populated subsystems, and the specific variant code associated with the genome in each of the populated subsystems. === NMPDR pathogen genome === The NMPDR is responsible for five classes of genomes: # Campylobacter jejuni # Listeria monocytogenes # Staphylococcus aureus # Streptococcus pneumoniae and Streptococcus pyogenes # Pathogenic Vibrio === Pair of Close Homologs (PCH) === The paper [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=EBI&pubmedid=10077608 The use of gene clusters to infer functional coupling] defines a Pair of Close Homologs as follows: <blockquote> We can also define the concept of “pairs of close homologs” (PCHs) as follows: genes (X′a, Y′a) from Ga and (X′b, Y′b) from Gb form a PCH if and only if X′a and Y′a are close, X′b and Y′b are close, X′a and X′b are recognizably similar, and Y′a and Y′b are recognizably similar. Here, we will consider two genes to be recognizably similar if their gene products produce fasta3 scores lower than 1.0 × 10−5. We use a scoring scheme analogous to the one described for PCBBHs to evaluate the connections between PCHs, except that if Ga and Gb are the same genome, we assign an arbitrary “same-genome score” (“same-genome” pairs cannot occur for PCBBHs by definition, but for PCHs they are possible). Unlike PCBBHs from two very close genomes for which contiguity is completely uninformative in the vast majority of cases, PCHs allow recognition of gene clusters that play similar (but usually not identical) roles (such as two transport cassettes containing pairs of homologs) in the same or similar organisms. The arbitrary “same-genome score” should, we believe, have a value that is high enough to rank such instances as significant. </blockquote> === PEG === A Protein Encoding Gene (PEG) is equivalent to a CDS (Coding Sequence). === Populated Subsystem === please see [[#Subsystem|Subsystem]] === SEED-Viewer === The SEED Viewer is a web-based application that allows browsing of SEED data structures. We use the SEED-Viewer to provide a public read-only version of the latest SEED data at: http://seed-viewer.theseed.org '''Please note''': The data is updated automatically every 24 hours. When citing or linking to the SEED please use this version. === Subsystem === A subsystem is a set of functional roles that an annotator has decided should be thought of as related. Frequently, subsystems represent the collection of [[#Functional_role|functional roles]] that make up a metabolic pathway, a complex (e.g., the ribosome), or a class of proteins (e.g., two-component signal-transduction proteins within Staphylococcus aureus). A '''populated subsystem''' is a subsystem with an attached spreadsheet. The rows of the spreadsheet represent genomes and the columns represent the functional roles of the spreadsheet. Each cell contains the identifiers of genes from the corresponding genome the implement the specific functional role. That is, a populated subsystem specifies which genes implement instances of the subsystem in each of the genomes. The rows of a populated genome are assigned '''variant codes''' which describe which of a set of possible variants of the subsystem exist within each genome (special codes expressing a total absence of the subsystem or remaining uncertainty exist). Construction of a large set of curated populated subsystems is at the center of the NMPDR and SEED annotation efforts. === Subsystem Clearing House === Since annotators can work on any machine (including the public SEED) the way to propagate subsystems is via http://clearinghouse.theseed.org/clearinghouse_browser.cgi? === Trial-SEED === A public, read-write copy of the SEED is made available on http://theseed.uchicago.edu/FIG/index.cgi '''Please note''': The data on this server is updated in irregular intervals. Users should not assume that annotations made on this system will persist. Please publish your annotations to the [[#Subsystem_clearing_house|Subsystem Clearing house]]. === Variant Code=== please see [[#Subsystem|Subsystem]] 0152fd7917344fe945789f3a577c7e055c3a63c5 1755 1754 2007-12-09T00:55:19Z FolkerMeyer 2 wikitext text/x-wiki === Annotators SEED === The master copy for all data in the SEED environment. Users can not access this password protected site. All annotations are made available via the [[#SEED-Viewer| SEED-Viewer]] and the [[#Trial-SEED|Trial-SEED]]. === Annotation === please see [[#Assigning_a_gene_function_and_annotation| Assigning a gene function and annotation]] === Assigning a gene function and annotation === Annotators assign gene functions to genes, and we call this process annotation. In most contexts, people use the term annotation to refer to assignments of function to the genes within a single organism. We certainly use the term in this sense, but we also use it to describe the process of assigning functions to corresponding genes from numerous genomes. Our basic approach to annotation is to ask our annotators to annotate the genes included in a [[#subsystem|Subsystem]] (e.g., glycolysis) across all genomes. This process of annotation of the genes within a subsystem across a set of genomes, rather than annotation of genes within a single genome, allows our annotators to focus on a constrained set of functional roles and attempt to accurately identify exactly what variant, if any, of a subsystem exists in each of the genomes. We use the term annotation to refer to assigning functions to genes (either within a single organism or to a constrained set of gene/protein families across a set of organisms). This activity certainly is closely related to the construction of subsystems and protein families (which we call FIGfams), but we will describe those activities elsewhere. === Assignment === please see [[#Assigning_a_gene_function_and_annotation| Assigning a gene function and annotation]] === Bidirectional Best Hit (BBH) === The paper [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=EBI&pubmedid=10077608 The use of gene clusters to infer functional coupling] defines a Bidirectional Best Hit or BBH as follows: <blockquote> Given two genes Xa and Xb from two genomes Ga and Gb, Xa and Xb are called a “bidirectional best hit (BBH)” if and only if recognizable similarity exists between them (in our case, we required fasta3 scores lower than 1.0 × 10−5), there is no gene Zb in Gb that is more similar than Xb is to Xa, and there is no gene Za in Ga that is more similar than Xa is to Xb. Genes (Xa, Ya) from Ga and (Xb, Yb) from Gb form a “pair of close bidirectional best hits (PCBBH)” if and only if Xa and Ya are close, Xb and Yb are close, Xa and Xb are a BBH, and Ya and Yb are a BBH. </blockquote> === Clearinghouse === please see [[#SubsystemClearinghouse|Subsystem Clearinghouse]] ===Feature=== A feature is a defined region in the DNA. A PEG is the most prevalent feature type in the SEED. Some other feature types include RNA, prophage and pathogenicity islands. The format for a feature ID is fig|genome_id.feature_abbreviation.feature_number (ie fig|83333.1.peg.100 ). === FIGfam === FIGfams are protein families generated by the Fellowship for Interpretation of Genomes (FIG). These families are based on the collection of subsystems, as well as correspondences between genes in closely related strains (we describe the construction of FIGfams in a separate SOP). The important properties of these families are as follows: # Two PEGs which both occur within a single FIGfam are believed to have the same function. # There is a decision procedure associated with the family which can be invoked to determine whether or not a gene can be “safely” assigned the function associated with the family. === FIG Identifier / FIG-IDs === We provide identifiers for genome sequences and features in the following form: {| ! Entity type !! key !! identifier |- | Genome || genome || fig<nowiki>|</nowiki>83331.1 |- | PEG || id || fig<nowiki>|</nowiki>83331.peg.123 |- | RNA feature || id || fig<nowiki>|</nowiki>83331.rna.1 |- |} (Please also see below for information on how to link to the SEED.) === Functional role === The concept of functional role is both basic and primitive in the sense that we will not pretend to offer a precise definition. It corresponds roughly to a single logical role that a gene or gene product may play in the operation of a cell. === Gene function === The function of a protein-encoding gene (PEG) is the functional role played by the product of the gene or an expression describing a set of roles played by the encoded protein. The operators used to construct expressions and the meanings associated with the operators are described in http://www.nmpdr.org/FIG/Html/SEED_functions.html Genes other than PEGs can also be assigned functions (e.g., SSU rRNA). However, in most cases the functions assigned to genes other than PEGs tend not to be problematic. === Linking to the SEED === We support linking to the SEED using a generic mechanism: Base URL: http://www.theseed.org/linkin.cgi? {| |+ Supported SEED Identifiers for external use ! Entity type !! key !! identifier !! Example |- | Genome || genome || fig<nowiki>|</nowiki>83331.1 || [[http://www.theseed.org/linkin.cgi?genome=fig|83333.1 http://www.theseed.org/linkin.cgi?genome=fig&#124;83333.1]] |- | PEG || id || fig<nowiki>|</nowiki>83331.peg.123 || [[http://www.theseed.org/linkin.cgi?id=fig|83333.1.peg.123 http://www.theseed.org/linkin.cgi?id=fig&#124;83333.1.peg.123]] |- | RNA feature || id || fig<nowiki>|</nowiki>83331.rna.1 || [[http://www.theseed.org/linkin.cgi?id=fig|83333.1.rna.1 http://www.theseed.org/linkin.cgi?id=fig&#124;83333.1.rna.1]] |- |} SEED identifiers contain the NCBI taxonomy ID, thus if the taxonomy ID changes, we need to update our internal data accordingly. To provide stable external identifiers, we keep a list of IDs that have changed and display warning message informing the user of the change and provide a link to the new version of the data requested. === Metabolic Reconstruction === When we use the term metabolic reconstruction of a given genome we will simply mean the set of populated subsystems that contain the genome, the PEGs (and their assigned functions) that are connected to functional roles in these populated subsystems, and the specific variant code associated with the genome in each of the populated subsystems. === NMPDR pathogen genome === The NMPDR is responsible for five classes of genomes: # Campylobacter jejuni # Listeria monocytogenes # Staphylococcus aureus # Streptococcus pneumoniae and Streptococcus pyogenes # Pathogenic Vibrio === Pair of Close Homologs (PCH) === The paper [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=EBI&pubmedid=10077608 The use of gene clusters to infer functional coupling] defines a Pair of Close Homologs as follows: <blockquote> We can also define the concept of “pairs of close homologs” (PCHs) as follows: genes (X′a, Y′a) from Ga and (X′b, Y′b) from Gb form a PCH if and only if X′a and Y′a are close, X′b and Y′b are close, X′a and X′b are recognizably similar, and Y′a and Y′b are recognizably similar. Here, we will consider two genes to be recognizably similar if their gene products produce fasta3 scores lower than 1.0 × 10−5. We use a scoring scheme analogous to the one described for PCBBHs to evaluate the connections between PCHs, except that if Ga and Gb are the same genome, we assign an arbitrary “same-genome score” (“same-genome” pairs cannot occur for PCBBHs by definition, but for PCHs they are possible). Unlike PCBBHs from two very close genomes for which contiguity is completely uninformative in the vast majority of cases, PCHs allow recognition of gene clusters that play similar (but usually not identical) roles (such as two transport cassettes containing pairs of homologs) in the same or similar organisms. The arbitrary “same-genome score” should, we believe, have a value that is high enough to rank such instances as significant. </blockquote> === PEG === A Protein Encoding Gene (PEG) is equivalent to a CDS (Coding Sequence). === Populated Subsystem === please see [[#Subsystem|Subsystem]] === SEED-Viewer === The SEED Viewer is a web-based application that allows browsing of SEED data structures. We use the SEED-Viewer to provide a public read-only version of the latest SEED data at: http://seed-viewer.theseed.org '''Please note''': The data is updated automatically every 24 hours. When citing or linking to the SEED please use this version. === Subsystem === A subsystem is a set of functional roles that an annotator has decided should be thought of as related. Frequently, subsystems represent the collection of [[#Functional_role|functional roles]] that make up a metabolic pathway, a complex (e.g., the ribosome), or a class of proteins (e.g., two-component signal-transduction proteins within Staphylococcus aureus). A '''populated subsystem''' is a subsystem with an attached spreadsheet. The rows of the spreadsheet represent genomes and the columns represent the functional roles of the spreadsheet. Each cell contains the identifiers of genes from the corresponding genome the implement the specific functional role. That is, a populated subsystem specifies which genes implement instances of the subsystem in each of the genomes. The rows of a populated genome are assigned '''variant codes''' which describe which of a set of possible variants of the subsystem exist within each genome (special codes expressing a total absence of the subsystem or remaining uncertainty exist). Construction of a large set of curated populated subsystems is at the center of the NMPDR and SEED annotation efforts. === Subsystem Clearing House === Since annotators can work on any machine (including the public SEED) the way to propagate subsystems is via http://clearinghouse.theseed.org/clearinghouse_browser.cgi? === Trial-SEED === A public, read-write copy of the SEED is made available on http://theseed.uchicago.edu/FIG/index.cgi '''Please note''': The data on this server is updated in irregular intervals. Users should not assume that annotations made on this system will persist. Please publish your annotations to the [[#Subsystem_clearing_house|Subsystem Clearing house]]. === Variant Code=== please see [[#Subsystem|Subsystem]] 663f6689f9a6c6597b2fe08324c968403074bea3 1756 1755 2007-12-09T00:57:14Z FolkerMeyer 2 wikitext text/x-wiki === Annotators SEED === The master copy for all data in the SEED environment. Users can not access this password protected site. All annotations are made available via the [[#SEED-Viewer| SEED-Viewer]] and the [[#Trial-SEED|Trial-SEED]]. === Annotation === please see [[#Assigning_a_gene_function_and_annotation| Assigning a gene function and annotation]] === Assigning a gene function and annotation === Annotators assign gene functions to genes, and we call this process annotation. In most contexts, people use the term annotation to refer to assignments of function to the genes within a single organism. We certainly use the term in this sense, but we also use it to describe the process of assigning functions to corresponding genes from numerous genomes. Our basic approach to annotation is to ask our annotators to annotate the genes included in a [[#subsystem|Subsystem]] (e.g., glycolysis) across all genomes. This process of annotation of the genes within a subsystem across a set of genomes, rather than annotation of genes within a single genome, allows our annotators to focus on a constrained set of functional roles and attempt to accurately identify exactly what variant, if any, of a subsystem exists in each of the genomes. We use the term annotation to refer to assigning functions to genes (either within a single organism or to a constrained set of gene/protein families across a set of organisms). This activity certainly is closely related to the construction of subsystems and protein families (which we call FIGfams), but we will describe those activities elsewhere. === Assignment === please see [[#Assigning_a_gene_function_and_annotation| Assigning a gene function and annotation]] === Bidirectional Best Hit (BBH) === The paper [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=EBI&pubmedid=10077608 The use of gene clusters to infer functional coupling] defines a Bidirectional Best Hit or BBH as follows: <blockquote> Given two genes Xa and Xb from two genomes Ga and Gb, Xa and Xb are called a “bidirectional best hit (BBH)” if and only if recognizable similarity exists between them (in our case, we required fasta3 scores lower than 1.0 × 10−5), there is no gene Zb in Gb that is more similar than Xb is to Xa, and there is no gene Za in Ga that is more similar than Xa is to Xb. Genes (Xa, Ya) from Ga and (Xb, Yb) from Gb form a “pair of close bidirectional best hits (PCBBH)” if and only if Xa and Ya are close, Xb and Yb are close, Xa and Xb are a BBH, and Ya and Yb are a BBH. </blockquote> === Clearinghouse === please see [[#SubsystemClearinghouse|Subsystem Clearinghouse]] ===Feature=== A feature is a defined region in the DNA. A PEG is the most prevalent feature type in the SEED. Some other feature types include RNA, prophage and pathogenicity islands. The format for a feature ID is fig|genome_id.feature_abbreviation.feature_number (ie fig|83333.1.peg.100 ). === FIGfam === FIGfams are protein families generated by the Fellowship for Interpretation of Genomes (FIG). These families are based on the collection of subsystems, as well as correspondences between genes in closely related strains (we describe the construction of FIGfams in a separate SOP). The important properties of these families are as follows: # Two PEGs which both occur within a single FIGfam are believed to have the same function. # There is a decision procedure associated with the family which can be invoked to determine whether or not a gene can be “safely” assigned the function associated with the family. === FIG Identifier / FIG-IDs === We provide identifiers for genome sequences and features in the following form: {| ! Entity type !! key !! identifier |- | Genome || genome || fig<nowiki>|</nowiki>83331.1 |- | PEG || id || fig<nowiki>|</nowiki>83331.peg.123 |- | RNA feature || id || fig<nowiki>|</nowiki>83331.rna.1 |- |} (Please also see below for information on how to link to the SEED.) === Functional role === The concept of functional role is both basic and primitive in the sense that we will not pretend to offer a precise definition. It corresponds roughly to a single logical role that a gene or gene product may play in the operation of a cell. === Gene function === The function of a protein-encoding gene (PEG) is the functional role played by the product of the gene or an expression describing a set of roles played by the encoded protein. The operators used to construct expressions and the meanings associated with the operators are described in http://www.nmpdr.org/FIG/Html/SEED_functions.html Genes other than PEGs can also be assigned functions (e.g., SSU rRNA). However, in most cases the functions assigned to genes other than PEGs tend not to be problematic. === Linking to the SEED === We support linking to the SEED using a generic mechanism: Base URL: http://www.theseed.org/linkin.cgi? {| |+ Supported SEED Identifiers for external use ! Entity type !! key !! identifier !! Example |- | Genome || genome || fig<nowiki>|</nowiki>83331.1 || [[http://www.theseed.org/linkin.cgi?genome=fig|83333.1 http://www.theseed.org/linkin.cgi?genome=fig&#124;83333.1]] |- | PEG || id || fig<nowiki>|</nowiki>83331.peg.123 || [[http://www.theseed.org/linkin.cgi?id=fig|83333.1.peg.123 http://www.theseed.org/linkin.cgi?id=fig&#124;83333.1.peg.123]] |- | RNA feature || id || fig<nowiki>|</nowiki>83331.rna.1 || [[http://www.theseed.org/linkin.cgi?id=fig|83333.1.rna.1 http://www.theseed.org/linkin.cgi?id=fig&#124;83333.1.rna.1]] |- |} SEED identifiers contain the NCBI taxonomy ID, thus if the taxonomy ID changes, we need to update our internal data accordingly. To provide stable external identifiers, we keep a list of IDs that have changed and display warning message informing the user of the change and provide a link to the new version of the data requested. === Metabolic Reconstruction === When we use the term metabolic reconstruction of a given genome we will simply mean the set of populated subsystems that contain the genome, the PEGs (and their assigned functions) that are connected to functional roles in these populated subsystems, and the specific variant code associated with the genome in each of the populated subsystems. === NMPDR pathogen genome === The NMPDR is responsible for five classes of genomes: # Campylobacter jejuni # Listeria monocytogenes # Staphylococcus aureus # Streptococcus pneumoniae and Streptococcus pyogenes # Pathogenic Vibrio === Pair of Close Homologs (PCH) === The paper [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=EBI&pubmedid=10077608 The use of gene clusters to infer functional coupling] defines a Pair of Close Homologs as follows: <blockquote> We can also define the concept of “pairs of close homologs” (PCHs) as follows: genes (X′a, Y′a) from Ga and (X′b, Y′b) from Gb form a PCH if and only if X′a and Y′a are close, X′b and Y′b are close, X′a and X′b are recognizably similar, and Y′a and Y′b are recognizably similar. Here, we will consider two genes to be recognizably similar if their gene products produce fasta3 scores lower than 1.0 × 10−5. We use a scoring scheme analogous to the one described for PCBBHs to evaluate the connections between PCHs, except that if Ga and Gb are the same genome, we assign an arbitrary “same-genome score” (“same-genome” pairs cannot occur for PCBBHs by definition, but for PCHs they are possible). Unlike PCBBHs from two very close genomes for which contiguity is completely uninformative in the vast majority of cases, PCHs allow recognition of gene clusters that play similar (but usually not identical) roles (such as two transport cassettes containing pairs of homologs) in the same or similar organisms. The arbitrary “same-genome score” should, we believe, have a value that is high enough to rank such instances as significant. </blockquote> === PEG === A Protein Encoding Gene (PEG) is equivalent to a CDS (Coding Sequence). === Populated Subsystem === please see [[#Subsystem|Subsystem]] === RAST === RAST or Rapid Annotation using Subsystem Technology is a rapid and very accurate annotation technology. We make a RAST server available for public use at [[http://rast.nmpdr.org]] === SEED-Viewer === The SEED Viewer is a web-based application that allows browsing of SEED data structures. We use the SEED-Viewer to provide a public read-only version of the latest SEED data at: http://seed-viewer.theseed.org '''Please note''': The data is updated automatically every 24 hours. When citing or linking to the SEED please use this version. === Subsystem === A subsystem is a set of functional roles that an annotator has decided should be thought of as related. Frequently, subsystems represent the collection of [[#Functional_role|functional roles]] that make up a metabolic pathway, a complex (e.g., the ribosome), or a class of proteins (e.g., two-component signal-transduction proteins within Staphylococcus aureus). A '''populated subsystem''' is a subsystem with an attached spreadsheet. The rows of the spreadsheet represent genomes and the columns represent the functional roles of the spreadsheet. Each cell contains the identifiers of genes from the corresponding genome the implement the specific functional role. That is, a populated subsystem specifies which genes implement instances of the subsystem in each of the genomes. The rows of a populated genome are assigned '''variant codes''' which describe which of a set of possible variants of the subsystem exist within each genome (special codes expressing a total absence of the subsystem or remaining uncertainty exist). Construction of a large set of curated populated subsystems is at the center of the NMPDR and SEED annotation efforts. === Subsystem Clearing House === Since annotators can work on any machine (including the public SEED) the way to propagate subsystems is via http://clearinghouse.theseed.org/clearinghouse_browser.cgi? === Trial-SEED === A public, read-write copy of the SEED is made available on http://theseed.uchicago.edu/FIG/index.cgi '''Please note''': The data on this server is updated in irregular intervals. Users should not assume that annotations made on this system will persist. Please publish your annotations to the [[#Subsystem_clearing_house|Subsystem Clearing house]]. === Variant Code=== please see [[#Subsystem|Subsystem]] 5c2c01a9270f171aa04fcef93f9dd4b05bb62549 1757 1756 2007-12-09T00:57:42Z FolkerMeyer 2 wikitext text/x-wiki === Annotators SEED === The master copy for all data in the SEED environment. Users can not access this password protected site. All annotations are made available via the [[#SEED-Viewer| SEED-Viewer]] and the [[#Trial-SEED|Trial-SEED]]. === Annotation === please see [[#Assigning_a_gene_function_and_annotation| Assigning a gene function and annotation]] === Assigning a gene function and annotation === Annotators assign gene functions to genes, and we call this process annotation. In most contexts, people use the term annotation to refer to assignments of function to the genes within a single organism. We certainly use the term in this sense, but we also use it to describe the process of assigning functions to corresponding genes from numerous genomes. Our basic approach to annotation is to ask our annotators to annotate the genes included in a [[#subsystem|Subsystem]] (e.g., glycolysis) across all genomes. This process of annotation of the genes within a subsystem across a set of genomes, rather than annotation of genes within a single genome, allows our annotators to focus on a constrained set of functional roles and attempt to accurately identify exactly what variant, if any, of a subsystem exists in each of the genomes. We use the term annotation to refer to assigning functions to genes (either within a single organism or to a constrained set of gene/protein families across a set of organisms). This activity certainly is closely related to the construction of subsystems and protein families (which we call FIGfams), but we will describe those activities elsewhere. === Assignment === please see [[#Assigning_a_gene_function_and_annotation| Assigning a gene function and annotation]] === Bidirectional Best Hit (BBH) === The paper [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=EBI&pubmedid=10077608 The use of gene clusters to infer functional coupling] defines a Bidirectional Best Hit or BBH as follows: <blockquote> Given two genes Xa and Xb from two genomes Ga and Gb, Xa and Xb are called a “bidirectional best hit (BBH)” if and only if recognizable similarity exists between them (in our case, we required fasta3 scores lower than 1.0 × 10−5), there is no gene Zb in Gb that is more similar than Xb is to Xa, and there is no gene Za in Ga that is more similar than Xa is to Xb. Genes (Xa, Ya) from Ga and (Xb, Yb) from Gb form a “pair of close bidirectional best hits (PCBBH)” if and only if Xa and Ya are close, Xb and Yb are close, Xa and Xb are a BBH, and Ya and Yb are a BBH. </blockquote> === Clearinghouse === please see [[#SubsystemClearinghouse|Subsystem Clearinghouse]] ===Feature=== A feature is a defined region in the DNA. A PEG is the most prevalent feature type in the SEED. Some other feature types include RNA, prophage and pathogenicity islands. The format for a feature ID is fig|genome_id.feature_abbreviation.feature_number (ie fig|83333.1.peg.100 ). === FIGfam === FIGfams are protein families generated by the Fellowship for Interpretation of Genomes (FIG). These families are based on the collection of subsystems, as well as correspondences between genes in closely related strains (we describe the construction of FIGfams in a separate SOP). The important properties of these families are as follows: # Two PEGs which both occur within a single FIGfam are believed to have the same function. # There is a decision procedure associated with the family which can be invoked to determine whether or not a gene can be “safely” assigned the function associated with the family. === FIG Identifier / FIG-IDs === We provide identifiers for genome sequences and features in the following form: {| ! Entity type !! key !! identifier |- | Genome || genome || fig<nowiki>|</nowiki>83331.1 |- | PEG || id || fig<nowiki>|</nowiki>83331.peg.123 |- | RNA feature || id || fig<nowiki>|</nowiki>83331.rna.1 |- |} (Please also see below for information on how to link to the SEED.) === Functional role === The concept of functional role is both basic and primitive in the sense that we will not pretend to offer a precise definition. It corresponds roughly to a single logical role that a gene or gene product may play in the operation of a cell. === Gene function === The function of a protein-encoding gene (PEG) is the functional role played by the product of the gene or an expression describing a set of roles played by the encoded protein. The operators used to construct expressions and the meanings associated with the operators are described in http://www.nmpdr.org/FIG/Html/SEED_functions.html Genes other than PEGs can also be assigned functions (e.g., SSU rRNA). However, in most cases the functions assigned to genes other than PEGs tend not to be problematic. === Linking to the SEED === We support linking to the SEED using a generic mechanism: Base URL: http://www.theseed.org/linkin.cgi? {| |+ Supported SEED Identifiers for external use ! Entity type !! key !! identifier !! Example |- | Genome || genome || fig<nowiki>|</nowiki>83331.1 || [[http://www.theseed.org/linkin.cgi?genome=fig|83333.1 http://www.theseed.org/linkin.cgi?genome=fig&#124;83333.1]] |- | PEG || id || fig<nowiki>|</nowiki>83331.peg.123 || [[http://www.theseed.org/linkin.cgi?id=fig|83333.1.peg.123 http://www.theseed.org/linkin.cgi?id=fig&#124;83333.1.peg.123]] |- | RNA feature || id || fig<nowiki>|</nowiki>83331.rna.1 || [[http://www.theseed.org/linkin.cgi?id=fig|83333.1.rna.1 http://www.theseed.org/linkin.cgi?id=fig&#124;83333.1.rna.1]] |- |} SEED identifiers contain the NCBI taxonomy ID, thus if the taxonomy ID changes, we need to update our internal data accordingly. To provide stable external identifiers, we keep a list of IDs that have changed and display warning message informing the user of the change and provide a link to the new version of the data requested. === Metabolic Reconstruction === When we use the term metabolic reconstruction of a given genome we will simply mean the set of populated subsystems that contain the genome, the PEGs (and their assigned functions) that are connected to functional roles in these populated subsystems, and the specific variant code associated with the genome in each of the populated subsystems. === NMPDR pathogen genome === The NMPDR is responsible for five classes of genomes: # Campylobacter jejuni # Listeria monocytogenes # Staphylococcus aureus # Streptococcus pneumoniae and Streptococcus pyogenes # Pathogenic Vibrio === Pair of Close Homologs (PCH) === The paper [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=EBI&pubmedid=10077608 The use of gene clusters to infer functional coupling] defines a Pair of Close Homologs as follows: <blockquote> We can also define the concept of “pairs of close homologs” (PCHs) as follows: genes (X′a, Y′a) from Ga and (X′b, Y′b) from Gb form a PCH if and only if X′a and Y′a are close, X′b and Y′b are close, X′a and X′b are recognizably similar, and Y′a and Y′b are recognizably similar. Here, we will consider two genes to be recognizably similar if their gene products produce fasta3 scores lower than 1.0 × 10−5. We use a scoring scheme analogous to the one described for PCBBHs to evaluate the connections between PCHs, except that if Ga and Gb are the same genome, we assign an arbitrary “same-genome score” (“same-genome” pairs cannot occur for PCBBHs by definition, but for PCHs they are possible). Unlike PCBBHs from two very close genomes for which contiguity is completely uninformative in the vast majority of cases, PCHs allow recognition of gene clusters that play similar (but usually not identical) roles (such as two transport cassettes containing pairs of homologs) in the same or similar organisms. The arbitrary “same-genome score” should, we believe, have a value that is high enough to rank such instances as significant. </blockquote> === PEG === A Protein Encoding Gene (PEG) is equivalent to a CDS (Coding Sequence). === Populated Subsystem === please see [[#Subsystem|Subsystem]] === RAST === RAST or Rapid Annotation using Subsystem Technology is a rapid and very accurate annotation technology. We make a RAST server available for public use at http://rast.nmpdr.org === SEED-Viewer === The SEED Viewer is a web-based application that allows browsing of SEED data structures. We use the SEED-Viewer to provide a public read-only version of the latest SEED data at: http://seed-viewer.theseed.org '''Please note''': The data is updated automatically every 24 hours. When citing or linking to the SEED please use this version. === Subsystem === A subsystem is a set of functional roles that an annotator has decided should be thought of as related. Frequently, subsystems represent the collection of [[#Functional_role|functional roles]] that make up a metabolic pathway, a complex (e.g., the ribosome), or a class of proteins (e.g., two-component signal-transduction proteins within Staphylococcus aureus). A '''populated subsystem''' is a subsystem with an attached spreadsheet. The rows of the spreadsheet represent genomes and the columns represent the functional roles of the spreadsheet. Each cell contains the identifiers of genes from the corresponding genome the implement the specific functional role. That is, a populated subsystem specifies which genes implement instances of the subsystem in each of the genomes. The rows of a populated genome are assigned '''variant codes''' which describe which of a set of possible variants of the subsystem exist within each genome (special codes expressing a total absence of the subsystem or remaining uncertainty exist). Construction of a large set of curated populated subsystems is at the center of the NMPDR and SEED annotation efforts. === Subsystem Clearing House === Since annotators can work on any machine (including the public SEED) the way to propagate subsystems is via http://clearinghouse.theseed.org/clearinghouse_browser.cgi? === Trial-SEED === A public, read-write copy of the SEED is made available on http://theseed.uchicago.edu/FIG/index.cgi '''Please note''': The data on this server is updated in irregular intervals. Users should not assume that annotations made on this system will persist. Please publish your annotations to the [[#Subsystem_clearing_house|Subsystem Clearing house]]. === Variant Code=== please see [[#Subsystem|Subsystem]] 35c6b267d930575b234524b4be9cc73cbdca315c 6 1446 1760 2007-12-18T02:21:04Z Marland 16 wikitext text/x-wiki da39a3ee5e6b4b0d3255bfef95601890afd80709 6 1448 1767 2007-12-18T02:27:51Z Marland 16 wikitext text/x-wiki da39a3ee5e6b4b0d3255bfef95601890afd80709 6 1449 1769 2007-12-18T02:29:03Z Marland 16 wikitext text/x-wiki da39a3ee5e6b4b0d3255bfef95601890afd80709 0 1 1772 1711 2007-12-31T18:39:13Z RobEdwards 14 wikitext text/x-wiki With the growing number of available genomes, the need for an environment to support effective comparative analysis increases. The original SEED Project was started in 2003 by the [http://thefig.info Fellowship for Interpretation of Genomes (FIG)] as a largely unfunded open source effort. Argonne National Laboratory and the University of Chicago joined the project, and now much of the activity occurs at those two institutions (as well as the University of Illinois at Urbana-Champaign, Hope college, San Diego State University, the Burnham Institute and a number of other institutions). The cooperative effort focuses on the development of the comparative genomics environment called the SEED and, more importantly, on the development of curated genomic data. We provide a [http://seed-viewer.theseed.org/ SEED-Viewer] that allows read-only access to the latest curated data sets. For users interested in editing and learning how to use the system, we provide the [http://theseed.uchicago.edu/FIG/index.cgi Trial-SEED]. As described in our [[Annotating_1000_genomes|manifesto]] the [[Glossary#Annotation|annotation]] is not performed on a gene by gene basis per genome, but rather by [[Glossary#Subsystem|subsystem]] by an expert curator across many genomes at a time. Answering numerous requests for automatic Seed-Quality annotations for more or less complete bacterial and archaeal genomes, we have established the free [http://rast.nmpdr.org RAST-Server] (RAST=Rapid Annotation using Subsytems Technology). Using similar technology, we make the [http://metagenomics.nmpdr.org Metagenomics-RAST-Server] freely available. We make all our software and data available for download and use on our [[DownloadPage]] page. * When using the SEED, please cite: Overbeek et al., [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16214803&query_hl=2&itool=pubmed_docsum|Nucleic Acids Res 33(17)], 2005 ([http://www.theseed.org/SubsystemPaperSupplementalMaterial/index.html Supplementary material]) * Our approaches to annotation, gene calling etc are outlined in a series of [[SOPs|Standard Operating Procedures]]. * Other [[papers that use the SEED]] 6598280442f27d99ae7d0f47abe5d9023103d403 0 1450 1773 2007-12-31T19:27:38Z RobEdwards 14 wikitext text/x-wiki = Papers related to the SEED = # Overbeek R, Begley T, Butler RM, Choudhuri JV, Chuang HY, Cohoon M, de Crécy-Lagard V, Diaz N, Disz T, Edwards R, Fonstein M, Frank ED, Gerdes S, Glass EM, Goesmann A, Hanson A, Iwata-Reuyl D, Jensen R, Jamshidi N, Krause L, Kubal M, Larsen N, Linke B, McHardy AC, Meyer F, Neuweger H, Olsen G, Olson R, Osterman A, Portnoy V, Pusch GD, Rodionov DA, Rückert C, Steiner J, Stevens R, Thiele I, Vassieva O, Ye Y, Zagnitko O, Vonstein V. (2005) Oct 7;33(17):5691-702. [http://www.ncbi.nlm.nih.gov/pubmed/16214803 PubMed] [http://nar.oxfordjournals.org/cgi/content/full/33/17/5691 NAR] [http://www.theseed.org/SubsystemPaperSupplementalMaterial/index.html SOM] # Angly, F.E., Felts, B., Breitbart, M., Salamon, P., Edwards, R.A., Carlson, C., Chan, A.M., Haynes, M., Kelley, S., Liu, H. et al. (2006) The marine viromes of four oceanic regions. PLoS Biol, 4. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=The%20marine%20viromes%20of%20four%20oceanic%20regions&cmd_current= PubMed] [http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pbio.0040368&ct=1 PLoS Biology] # DeLong, E.F., Preston, C.M., Mincer, T., Rich, V., Hallam, S.J., Frigaard, N.U., Martinez, A., Sullivan, M.B., Edwards, R., Brito, B.R. et al. (2006) Community genomics among stratified microbial assemblages in the ocean's interior. Science, 311, 496-503. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=Community%20genomics%20among%20stratified%20microbial%20assemblages%20in%20the%20ocean%27s%20interior&cmd_current= PubMed] # Edwards, R.A., Rodriguez-Brito, B., Wegley, L., Haynes, M., Breitbart, M., Peterson, D.M., Saar, M.O., Alexander, S., Alexander, E.C., Jr. and Rohwer, F. (2006) Using pyrosequencing to shed light on deep mine microbial ecology. BMC Genomics, 7, 57. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=16549033&cmd_current= PubMed] [http://www.biomedcentral.com/1471-2164/7/57 BioMed Central] # Krause, L., Diaz, N.N., Bartels, D., Edwards, R.A., Puhler, A., Rohwer, F., Meyer, F. and Stoye, J. (2006) Finding novel genes in bacterial communities isolated from the environment. Bioinformatics, 22, e281. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=16873483&cmd_current= PubMed] [http://bioinformatics.oxfordjournals.org/cgi/reprint/22/14/e281 NAR] # Rodriguez-Brito, B., Rohwer, F. and Edwards, R. (2006) An application of statistics to comparative metagenomics. BMC Bioinformatics, 7, 162. # Fierer, N., Breitbart, M., Nulton, J., Salamon, P., Lozupone, P., Jones, R., Robeson, M., Edwards, R., Felts, B., Rayhawk, S. et al. (2007) Metagenomic and small-subunit RNA surveys reveal the high genetic diversity of bacteria, archaea, fungi, and viruses in soil. Appl Environ Microbiol, 73, 7059-7066. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17827313&cmd_current= PubMed] [http://aem.asm.org/cgi/content/full/73/21/7059?view=long&pmid=17827313 AEM] # McNeil LK, Reich C, Aziz RK, Bartels D, Cohoon M, Disz T, Edwards RA, Gerdes SY, Hwang K, Kubal M, Margaryan GR, Meyer F, Mihalo W, Olsen GJ, Olson R, Osterman AL, Paarmann D, Paczian T, Parrello B, Pusch GD, Rodionov DA, Shi X, Vassieva O, Vonstein V, Zagnitko OP, Xia F, Zinner J, Overbeek R, Stevens R.(2007) The National Microbial Pathogen Database Resource (NMPDR): A genomics platform based on subsystem annotation. Nucleic Acids Res. 2007 Jan;35(Database issue):D347-53 [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17145713 PubMed] [http://nar.oxfordjournals.org/cgi/content/full/35/suppl_1/D347 NAR] # Wegley, L., Breitbart, M., Edwards, R. and Rohwer, F. (2007) Functional and taxonimic analysis of coral-associated microbes using metagenomic analysis. Environ Microbiol, 9, 2707-2719. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17922755&cmd_current= PubMed] [http://www.blackwell-synergy.com/doi/abs/10.1111/j.1462-2920.2007.01383.x Environ Microbiol] ==In press== # Desnues CG, B Rodriguez-Brito, S Rayhawk, S Kelley, T Tran, M Haynes, H Liu, D Hall, FE Angly, RA Edwards, RB Thurber, P Reid, J Siefert, V Souza, DL Valentine, BK Swan, M Breitbart, F Rohwer (2008; accepted) Biodiversity and biogeography of phages in modern stromatolites and thrombolites. Nature In press. # Mou, X.S., S., Edwards, R.A., Hodson, R.E. and Moran, M.A. (2007) Generalist Species Dominate Bacterial Carbon Processing in the Coastal Ocean. Nature, In Press. # Breitbart M, M Haynes, S Kelley, F Angly, R Edwards, B Felts, JM Mahaffy, J Mueller, J Nulton, S Rayhawk, B Rodriguez-Brito, P Salamon, F Rohwer (2008) Viral diversity and dynamics in an infant's gut. ~~ 9511866cdf30fcc275a8f5b35d4a9ce9b7e51272 0 1450 1774 1773 2007-12-31T19:28:05Z RobEdwards 14 wikitext text/x-wiki # Overbeek R, Begley T, Butler RM, Choudhuri JV, Chuang HY, Cohoon M, de Crécy-Lagard V, Diaz N, Disz T, Edwards R, Fonstein M, Frank ED, Gerdes S, Glass EM, Goesmann A, Hanson A, Iwata-Reuyl D, Jensen R, Jamshidi N, Krause L, Kubal M, Larsen N, Linke B, McHardy AC, Meyer F, Neuweger H, Olsen G, Olson R, Osterman A, Portnoy V, Pusch GD, Rodionov DA, Rückert C, Steiner J, Stevens R, Thiele I, Vassieva O, Ye Y, Zagnitko O, Vonstein V. (2005) Oct 7;33(17):5691-702. [http://www.ncbi.nlm.nih.gov/pubmed/16214803 PubMed] [http://nar.oxfordjournals.org/cgi/content/full/33/17/5691 NAR] [http://www.theseed.org/SubsystemPaperSupplementalMaterial/index.html SOM] # Angly, F.E., Felts, B., Breitbart, M., Salamon, P., Edwards, R.A., Carlson, C., Chan, A.M., Haynes, M., Kelley, S., Liu, H. et al. (2006) The marine viromes of four oceanic regions. PLoS Biol, 4. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=The%20marine%20viromes%20of%20four%20oceanic%20regions&cmd_current= PubMed] [http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pbio.0040368&ct=1 PLoS Biology] # DeLong, E.F., Preston, C.M., Mincer, T., Rich, V., Hallam, S.J., Frigaard, N.U., Martinez, A., Sullivan, M.B., Edwards, R., Brito, B.R. et al. (2006) Community genomics among stratified microbial assemblages in the ocean's interior. Science, 311, 496-503. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=Community%20genomics%20among%20stratified%20microbial%20assemblages%20in%20the%20ocean%27s%20interior&cmd_current= PubMed] # Edwards, R.A., Rodriguez-Brito, B., Wegley, L., Haynes, M., Breitbart, M., Peterson, D.M., Saar, M.O., Alexander, S., Alexander, E.C., Jr. and Rohwer, F. (2006) Using pyrosequencing to shed light on deep mine microbial ecology. BMC Genomics, 7, 57. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=16549033&cmd_current= PubMed] [http://www.biomedcentral.com/1471-2164/7/57 BioMed Central] # Krause, L., Diaz, N.N., Bartels, D., Edwards, R.A., Puhler, A., Rohwer, F., Meyer, F. and Stoye, J. (2006) Finding novel genes in bacterial communities isolated from the environment. Bioinformatics, 22, e281. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=16873483&cmd_current= PubMed] [http://bioinformatics.oxfordjournals.org/cgi/reprint/22/14/e281 NAR] # Rodriguez-Brito, B., Rohwer, F. and Edwards, R. (2006) An application of statistics to comparative metagenomics. BMC Bioinformatics, 7, 162. # Fierer, N., Breitbart, M., Nulton, J., Salamon, P., Lozupone, P., Jones, R., Robeson, M., Edwards, R., Felts, B., Rayhawk, S. et al. (2007) Metagenomic and small-subunit RNA surveys reveal the high genetic diversity of bacteria, archaea, fungi, and viruses in soil. Appl Environ Microbiol, 73, 7059-7066. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17827313&cmd_current= PubMed] [http://aem.asm.org/cgi/content/full/73/21/7059?view=long&pmid=17827313 AEM] # McNeil LK, Reich C, Aziz RK, Bartels D, Cohoon M, Disz T, Edwards RA, Gerdes SY, Hwang K, Kubal M, Margaryan GR, Meyer F, Mihalo W, Olsen GJ, Olson R, Osterman AL, Paarmann D, Paczian T, Parrello B, Pusch GD, Rodionov DA, Shi X, Vassieva O, Vonstein V, Zagnitko OP, Xia F, Zinner J, Overbeek R, Stevens R.(2007) The National Microbial Pathogen Database Resource (NMPDR): A genomics platform based on subsystem annotation. Nucleic Acids Res. 2007 Jan;35(Database issue):D347-53 [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17145713 PubMed] [http://nar.oxfordjournals.org/cgi/content/full/35/suppl_1/D347 NAR] # Wegley, L., Breitbart, M., Edwards, R. and Rohwer, F. (2007) Functional and taxonimic analysis of coral-associated microbes using metagenomic analysis. Environ Microbiol, 9, 2707-2719. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17922755&cmd_current= PubMed] [http://www.blackwell-synergy.com/doi/abs/10.1111/j.1462-2920.2007.01383.x Environ Microbiol] ==In press== # Desnues CG, B Rodriguez-Brito, S Rayhawk, S Kelley, T Tran, M Haynes, H Liu, D Hall, FE Angly, RA Edwards, RB Thurber, P Reid, J Siefert, V Souza, DL Valentine, BK Swan, M Breitbart, F Rohwer (2008; accepted) Biodiversity and biogeography of phages in modern stromatolites and thrombolites. Nature In press. # Mou, X.S., S., Edwards, R.A., Hodson, R.E. and Moran, M.A. (2007) Generalist Species Dominate Bacterial Carbon Processing in the Coastal Ocean. Nature, In Press. # Breitbart M, M Haynes, S Kelley, F Angly, R Edwards, B Felts, JM Mahaffy, J Mueller, J Nulton, S Rayhawk, B Rodriguez-Brito, P Salamon, F Rohwer (2008) Viral diversity and dynamics in an infant's gut. 223e0d69b0e5a3f354c41cb7a0cee4d08efd805f 1775 1774 2007-12-31T19:30:29Z RobEdwards 14 wikitext text/x-wiki # Overbeek R, Begley T, Butler RM, Choudhuri JV, Chuang HY, Cohoon M, de Crécy-Lagard V, Diaz N, Disz T, Edwards R, Fonstein M, Frank ED, Gerdes S, Glass EM, Goesmann A, Hanson A, Iwata-Reuyl D, Jensen R, Jamshidi N, Krause L, Kubal M, Larsen N, Linke B, McHardy AC, Meyer F, Neuweger H, Olsen G, Olson R, Osterman A, Portnoy V, Pusch GD, Rodionov DA, Rückert C, Steiner J, Stevens R, Thiele I, Vassieva O, Ye Y, Zagnitko O, Vonstein V. (2005) Oct 7;33(17):5691-702. [http://www.ncbi.nlm.nih.gov/pubmed/16214803 PubMed] [http://nar.oxfordjournals.org/cgi/content/full/33/17/5691 NAR] [http://www.theseed.org/SubsystemPaperSupplementalMaterial/index.html Supplemental Online Material] # Angly, F.E., Felts, B., Breitbart, M., Salamon, P., Edwards, R.A., Carlson, C., Chan, A.M., Haynes, M., Kelley, S., Liu, H. et al. (2006) The marine viromes of four oceanic regions. PLoS Biol, 4. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=The%20marine%20viromes%20of%20four%20oceanic%20regions&cmd_current= PubMed] [http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pbio.0040368&ct=1 PLoS Biology] # DeLong, E.F., Preston, C.M., Mincer, T., Rich, V., Hallam, S.J., Frigaard, N.U., Martinez, A., Sullivan, M.B., Edwards, R., Brito, B.R. et al. (2006) Community genomics among stratified microbial assemblages in the ocean's interior. Science, 311, 496-503. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=Community%20genomics%20among%20stratified%20microbial%20assemblages%20in%20the%20ocean%27s%20interior&cmd_current= PubMed] # Edwards, R.A., Rodriguez-Brito, B., Wegley, L., Haynes, M., Breitbart, M., Peterson, D.M., Saar, M.O., Alexander, S., Alexander, E.C., Jr. and Rohwer, F. (2006) Using pyrosequencing to shed light on deep mine microbial ecology. BMC Genomics, 7, 57. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=16549033&cmd_current= PubMed] [http://www.biomedcentral.com/1471-2164/7/57 BioMed Central] # Krause, L., Diaz, N.N., Bartels, D., Edwards, R.A., Puhler, A., Rohwer, F., Meyer, F. and Stoye, J. (2006) Finding novel genes in bacterial communities isolated from the environment. Bioinformatics, 22, e281. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=16873483&cmd_current= PubMed] [http://bioinformatics.oxfordjournals.org/cgi/reprint/22/14/e281 NAR] # Rodriguez-Brito, B., Rohwer, F. and Edwards, R. (2006) An application of statistics to comparative metagenomics. BMC Bioinformatics, 7, 162. # Fierer, N., Breitbart, M., Nulton, J., Salamon, P., Lozupone, P., Jones, R., Robeson, M., Edwards, R., Felts, B., Rayhawk, S. et al. (2007) Metagenomic and small-subunit RNA surveys reveal the high genetic diversity of bacteria, archaea, fungi, and viruses in soil. Appl Environ Microbiol, 73, 7059-7066. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17827313&cmd_current= PubMed] [http://aem.asm.org/cgi/content/full/73/21/7059?view=long&pmid=17827313 AEM] # McNeil LK, Reich C, Aziz RK, Bartels D, Cohoon M, Disz T, Edwards RA, Gerdes SY, Hwang K, Kubal M, Margaryan GR, Meyer F, Mihalo W, Olsen GJ, Olson R, Osterman AL, Paarmann D, Paczian T, Parrello B, Pusch GD, Rodionov DA, Shi X, Vassieva O, Vonstein V, Zagnitko OP, Xia F, Zinner J, Overbeek R, Stevens R.(2007) The National Microbial Pathogen Database Resource (NMPDR): A genomics platform based on subsystem annotation. Nucleic Acids Res. 2007 Jan;35(Database issue):D347-53 [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17145713 PubMed] [http://nar.oxfordjournals.org/cgi/content/full/35/suppl_1/D347 NAR] # Wegley, L., Breitbart, M., Edwards, R. and Rohwer, F. (2007) Functional and taxonimic analysis of coral-associated microbes using metagenomic analysis. Environ Microbiol, 9, 2707-2719. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17922755&cmd_current= PubMed] [http://www.blackwell-synergy.com/doi/abs/10.1111/j.1462-2920.2007.01383.x Environ Microbiol] ==In press== # Desnues CG, B Rodriguez-Brito, S Rayhawk, S Kelley, T Tran, M Haynes, H Liu, D Hall, FE Angly, RA Edwards, RB Thurber, P Reid, J Siefert, V Souza, DL Valentine, BK Swan, M Breitbart, F Rohwer (2008; accepted) Biodiversity and biogeography of phages in modern stromatolites and thrombolites. Nature In press. # Mou, X.S., S., Edwards, R.A., Hodson, R.E. and Moran, M.A. (2007) Generalist Species Dominate Bacterial Carbon Processing in the Coastal Ocean. Nature, In Press. # Breitbart M, M Haynes, S Kelley, F Angly, R Edwards, B Felts, JM Mahaffy, J Mueller, J Nulton, S Rayhawk, B Rodriguez-Brito, P Salamon, F Rohwer (2008) Viral diversity and dynamics in an infant's gut. f2d0e23e3a7e3f1f36566c618de595f507af1ff9 1776 1775 2007-12-31T21:40:23Z RobEdwards 14 wikitext text/x-wiki # Overbeek R, Begley T, Butler RM, Choudhuri JV, Chuang HY, Cohoon M, de Crécy-Lagard V, Diaz N, Disz T, Edwards R, Fonstein M, Frank ED, Gerdes S, Glass EM, Goesmann A, Hanson A, Iwata-Reuyl D, Jensen R, Jamshidi N, Krause L, Kubal M, Larsen N, Linke B, McHardy AC, Meyer F, Neuweger H, Olsen G, Olson R, Osterman A, Portnoy V, Pusch GD, Rodionov DA, Rückert C, Steiner J, Stevens R, Thiele I, Vassieva O, Ye Y, Zagnitko O, Vonstein V. (2005) Oct 7;33(17):5691-702. [http://www.ncbi.nlm.nih.gov/pubmed/16214803 PubMed] [http://nar.oxfordjournals.org/cgi/content/full/33/17/5691 NAR] [http://www.theseed.org/SubsystemPaperSupplementalMaterial/index.html Supplemental Online Material] # Angly, F.E., Felts, B., Breitbart, M., Salamon, P., Edwards, R.A., Carlson, C., Chan, A.M., Haynes, M., Kelley, S., Liu, H. et al. (2006) The marine viromes of four oceanic regions. PLoS Biol, 4. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=The%20marine%20viromes%20of%20four%20oceanic%20regions&cmd_current= PubMed] [http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pbio.0040368&ct=1 PLoS Biology] # DeLong, E.F., Preston, C.M., Mincer, T., Rich, V., Hallam, S.J., Frigaard, N.U., Martinez, A., Sullivan, M.B., Edwards, R., Brito, B.R. et al. (2006) Community genomics among stratified microbial assemblages in the ocean's interior. Science, 311, 496-503. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=Community%20genomics%20among%20stratified%20microbial%20assemblages%20in%20the%20ocean%27s%20interior&cmd_current= PubMed] # Edwards, R.A., Rodriguez-Brito, B., Wegley, L., Haynes, M., Breitbart, M., Peterson, D.M., Saar, M.O., Alexander, S., Alexander, E.C., Jr. and Rohwer, F. (2006) Using pyrosequencing to shed light on deep mine microbial ecology. BMC Genomics, 7, 57. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=16549033&cmd_current= PubMed] [http://www.biomedcentral.com/1471-2164/7/57 BioMed Central] # Krause, L., Diaz, N.N., Bartels, D., Edwards, R.A., Puhler, A., Rohwer, F., Meyer, F. and Stoye, J. (2006) Finding novel genes in bacterial communities isolated from the environment. Bioinformatics, 22, e281. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=16873483&cmd_current= PubMed] [http://bioinformatics.oxfordjournals.org/cgi/reprint/22/14/e281 NAR] # Rodriguez-Brito, B., Rohwer, F. and Edwards, R. (2006) An application of statistics to comparative metagenomics. BMC Bioinformatics, 7, 162. # El Yacoubi B, Bonnett S, Anderson JN, Swairjo MA, Iwata-Reuyl D, de Crécy-Lagard V. (2006) Discovery of a new prokaryotic type I GTP cyclohydrolase family. J Biol Chem. Dec 8;281(49):37586-93. Epub 2006 Oct 10. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17032654&cmd_current= PubMed] [http://www.jbc.org/cgi/content/full/281/49/37586 JBC]# Fierer, N., Breitbart, M., Nulton, J., Salamon, P., Lozupone, P., Jones, R., Robeson, M., Edwards, R., Felts, B., Rayhawk, S. et al. (2007) Metagenomic and small-subunit RNA surveys reveal the high genetic diversity of bacteria, archaea, fungi, and viruses in soil. Appl Environ Microbiol, 73, 7059-7066. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17827313&cmd_current= PubMed] [http://aem.asm.org/cgi/content/full/73/21/7059?view=long&pmid=17827313 AEM] # de Crecy-Lagard V, Hanson AD. (2007) Finding novel metabolic genes through plant-prokaryote phylogenomics. Trends Microbiol. Dec;15(12):563-70. Epub 2007 Nov 9. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17997099&cmd_current= PubMed] [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TD0-4R3BW70-1&_user=10&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=45c7be528111535816858125516a93ad Trends] # de Crecy-Lagard V, El Yacoubi B, de la Garza RD, Noiriel A, Hanson AD. (2007) Comparative genomics of bacterial and plant folate synthesis and salvage: predictions and validations. BMC Genomics. Jul 23;8:245.[http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17645794&cmd_current= PubMed] [http://www.biomedcentral.com/1471-2164/8/245 Biomed Central] # McNeil LK, Reich C, Aziz RK, Bartels D, Cohoon M, Disz T, Edwards RA, Gerdes SY, Hwang K, Kubal M, Margaryan GR, Meyer F, Mihalo W, Olsen GJ, Olson R, Osterman AL, Paarmann D, Paczian T, Parrello B, Pusch GD, Rodionov DA, Shi X, Vassieva O, Vonstein V, Zagnitko OP, Xia F, Zinner J, Overbeek R, Stevens R.(2007) The National Microbial Pathogen Database Resource (NMPDR): A genomics platform based on subsystem annotation. Nucleic Acids Res. 2007 Jan;35(Database issue):D347-53 [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17145713 PubMed] [http://nar.oxfordjournals.org/cgi/content/full/35/suppl_1/D347 NAR] # Wegley, L., Breitbart, M., Edwards, R. and Rohwer, F. (2007) Functional and taxonimic analysis of coral-associated microbes using metagenomic analysis. Environ Microbiol, 9, 2707-2719. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17922755&cmd_current= PubMed] [http://www.blackwell-synergy.com/doi/abs/10.1111/j.1462-2920.2007.01383.x Environ Microbiol] ==In press== # Desnues CG, B Rodriguez-Brito, S Rayhawk, S Kelley, T Tran, M Haynes, H Liu, D Hall, FE Angly, RA Edwards, RB Thurber, P Reid, J Siefert, V Souza, DL Valentine, BK Swan, M Breitbart, F Rohwer (2008; accepted) Biodiversity and biogeography of phages in modern stromatolites and thrombolites. Nature In press. # Mou, X.S., S., Edwards, R.A., Hodson, R.E. and Moran, M.A. (2007) Generalist Species Dominate Bacterial Carbon Processing in the Coastal Ocean. Nature, In Press. # Breitbart M, M Haynes, S Kelley, F Angly, R Edwards, B Felts, JM Mahaffy, J Mueller, J Nulton, S Rayhawk, B Rodriguez-Brito, P Salamon, F Rohwer (2008) Viral diversity and dynamics in an infant's gut. 5c1910ce61aad86b7208f4e5f02ff243e18fa4a4 1777 1776 2007-12-31T21:43:19Z RobEdwards 14 wikitext text/x-wiki # Overbeek R, Begley T, Butler RM, Choudhuri JV, Chuang HY, Cohoon M, de Crécy-Lagard V, Diaz N, Disz T, Edwards R, Fonstein M, Frank ED, Gerdes S, Glass EM, Goesmann A, Hanson A, Iwata-Reuyl D, Jensen R, Jamshidi N, Krause L, Kubal M, Larsen N, Linke B, McHardy AC, Meyer F, Neuweger H, Olsen G, Olson R, Osterman A, Portnoy V, Pusch GD, Rodionov DA, Rückert C, Steiner J, Stevens R, Thiele I, Vassieva O, Ye Y, Zagnitko O, Vonstein V. (2005) Oct 7;33(17):5691-702. [http://www.ncbi.nlm.nih.gov/pubmed/16214803 PubMed] [http://nar.oxfordjournals.org/cgi/content/full/33/17/5691 NAR] [http://www.theseed.org/SubsystemPaperSupplementalMaterial/index.html Supplemental Online Material] # Angly, F.E., Felts, B., Breitbart, M., Salamon, P., Edwards, R.A., Carlson, C., Chan, A.M., Haynes, M., Kelley, S., Liu, H. et al. (2006) The marine viromes of four oceanic regions. PLoS Biol, 4. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=The%20marine%20viromes%20of%20four%20oceanic%20regions&cmd_current= PubMed] [http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pbio.0040368&ct=1 PLoS Biology] # DeLong, E.F., Preston, C.M., Mincer, T., Rich, V., Hallam, S.J., Frigaard, N.U., Martinez, A., Sullivan, M.B., Edwards, R., Brito, B.R. et al. (2006) Community genomics among stratified microbial assemblages in the ocean's interior. Science, 311, 496-503. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=Community%20genomics%20among%20stratified%20microbial%20assemblages%20in%20the%20ocean%27s%20interior&cmd_current= PubMed] # Edwards, R.A., Rodriguez-Brito, B., Wegley, L., Haynes, M., Breitbart, M., Peterson, D.M., Saar, M.O., Alexander, S., Alexander, E.C., Jr. and Rohwer, F. (2006) Using pyrosequencing to shed light on deep mine microbial ecology. BMC Genomics, 7, 57. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=16549033&cmd_current= PubMed] [http://www.biomedcentral.com/1471-2164/7/57 BioMed Central] # Krause, L., Diaz, N.N., Bartels, D., Edwards, R.A., Puhler, A., Rohwer, F., Meyer, F. and Stoye, J. (2006) Finding novel genes in bacterial communities isolated from the environment. Bioinformatics, 22, e281. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=16873483&cmd_current= PubMed] [http://bioinformatics.oxfordjournals.org/cgi/reprint/22/14/e281 NAR] # Rodriguez-Brito, B., Rohwer, F. and Edwards, R. (2006) An application of statistics to comparative metagenomics. BMC Bioinformatics, 7, 162. # El Yacoubi B, Bonnett S, Anderson JN, Swairjo MA, Iwata-Reuyl D, de Crécy-Lagard V. (2006) Discovery of a new prokaryotic type I GTP cyclohydrolase family. J Biol Chem. Dec 8;281(49):37586-93. Epub 2006 Oct 10. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17032654&cmd_current= PubMed] [http://www.jbc.org/cgi/content/full/281/49/37586 JBC]# Fierer, N., Breitbart, M., Nulton, J., Salamon, P., Lozupone, P., Jones, R., Robeson, M., Edwards, R., Felts, B., Rayhawk, S. et al. (2007) Metagenomic and small-subunit RNA surveys reveal the high genetic diversity of bacteria, archaea, fungi, and viruses in soil. Appl Environ Microbiol, 73, 7059-7066. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17827313&cmd_current= PubMed] [http://aem.asm.org/cgi/content/full/73/21/7059?view=long&pmid=17827313 AEM] # de Crecy-Lagard V, Hanson AD. (2007) Finding novel metabolic genes through plant-prokaryote phylogenomics. Trends Microbiol. Dec;15(12):563-70. Epub 2007 Nov 9. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17997099&cmd_current= PubMed] [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TD0-4R3BW70-1&_user=10&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=45c7be528111535816858125516a93ad Trends] # de Crecy-Lagard V, El Yacoubi B, de la Garza RD, Noiriel A, Hanson AD. (2007) Comparative genomics of bacterial and plant folate synthesis and salvage: predictions and validations. BMC Genomics. Jul 23;8:245.[http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17645794&cmd_current= PubMed] [http://www.biomedcentral.com/1471-2164/8/245 Biomed Central] # McNeil LK, Reich C, Aziz RK, Bartels D, Cohoon M, Disz T, Edwards RA, Gerdes SY, Hwang K, Kubal M, Margaryan GR, Meyer F, Mihalo W, Olsen GJ, Olson R, Osterman AL, Paarmann D, Paczian T, Parrello B, Pusch GD, Rodionov DA, Shi X, Vassieva O, Vonstein V, Zagnitko OP, Xia F, Zinner J, Overbeek R, Stevens R.(2007) The National Microbial Pathogen Database Resource (NMPDR): A genomics platform based on subsystem annotation. Nucleic Acids Res. 2007 Jan;35(Database issue):D347-53 [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17145713 PubMed] [http://nar.oxfordjournals.org/cgi/content/full/35/suppl_1/D347 NAR] # Wegley, L., Breitbart, M., Edwards, R. and Rohwer, F. (2007) Functional and taxonimic analysis of coral-associated microbes using metagenomic analysis. 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Comparative genomics and experimental characterization of N-acetylglucosamine utilization pathway of Shewanella oneidensis. J Biol Chem 281:29872-85. PMID: 16857666 5. Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S., (2006). Experimental and computational assessment of conditionally essential genes in E. coli. J Bacteriol. 188(23):8259-71. PMID: 17012394 6. Gerdes, S., R. Edwards, M. Kubal, M. Fonstein, R. Stevens, and A. Osterman. (2006). Essential genes on metabolic maps. Curr Opin Biotechnol 17:448-56. PMID: 16978855. 7. Osterman, A., and T. Begley. (2007). A Subsystems-based approach to the identification of drug targets in bacterial pathogens, p. 132-170. In H.Boshoff and C.Barry (ed.), Progress in Drug Research, vol. 64. Birkhauser Verlag, Basel. PMID: 17195474 8. Dmitry A. Rodionov, Oleg V. Kurnasov, Boguslaw Stec, Yan Wang, Mary F. Roberts, and Andrei L. Osterman (2007) Genomic identification and in vitro reconstitution of a complete biosynthetic pathway for the osmolyte di-myo-inositol-phosphate. . Proc Natl Acad Sci U S A. Mar 13;104(11):4279-84. PMID: 17360515 Gupta N, Tanner S, Jaitly N, Adkins JN, Lipton M, Edwards R, Romine M, Osterman A, Bafna V, Smith RD, Pevzner PA. (2007) Whole proteome analysis of post-translational modifications: Applications of mass-spectrometry for proteogenomic annotation.Genome Res. Sep;17(9):1362-77. Epub 2007 Aug 9. PMID: 17690205 # JR. Yates III and AL. Osterman (2007) Introduction: advances in genomics and proteomics. Chem Rev. Aug;107(8):3363-6. Epub 2007 Jul 21. [http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/cr068201u ACS] # Yang C, Rodionov DA, Rodionova IA, Li X, Osterman AL. (2007) Glycerate 2-kinase of Thermotoga maritima and genomic reconstruction of related metabolic pathways., J Bacteriol. 2007 Dec 21; [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=18156253&cmd_current= PubMed] [http://jb.asm.org/cgi/reprint/JB.01469-07v1?view=long&pmid=18156253 JBact] ==In press== # Desnues CG, B Rodriguez-Brito, S Rayhawk, S Kelley, T Tran, M Haynes, H Liu, D Hall, FE Angly, RA Edwards, RB Thurber, P Reid, J Siefert, V Souza, DL Valentine, BK Swan, M Breitbart, F Rohwer (2008; accepted) Biodiversity and biogeography of phages in modern stromatolites and thrombolites. Nature In press. # Mou, X.S., S., Edwards, R.A., Hodson, R.E. and Moran, M.A. (2007) Generalist Species Dominate Bacterial Carbon Processing in the Coastal Ocean. Nature, In Press. # Breitbart M, M Haynes, S Kelley, F Angly, R Edwards, B Felts, JM Mahaffy, J Mueller, J Nulton, S Rayhawk, B Rodriguez-Brito, P Salamon, F Rohwer (2008) Viral diversity and dynamics in an infant's gut. 74a9751859621a54e4c406876ad89f0ba3450337 1778 1777 2007-12-31T21:46:40Z RobEdwards 14 wikitext text/x-wiki # Overbeek R, Begley T, Butler RM, Choudhuri JV, Chuang HY, Cohoon M, de Crécy-Lagard V, Diaz N, Disz T, Edwards R, Fonstein M, Frank ED, Gerdes S, Glass EM, Goesmann A, Hanson A, Iwata-Reuyl D, Jensen R, Jamshidi N, Krause L, Kubal M, Larsen N, Linke B, McHardy AC, Meyer F, Neuweger H, Olsen G, Olson R, Osterman A, Portnoy V, Pusch GD, Rodionov DA, Rückert C, Steiner J, Stevens R, Thiele I, Vassieva O, Ye Y, Zagnitko O, Vonstein V. (2005) Oct 7;33(17):5691-702. [http://www.ncbi.nlm.nih.gov/pubmed/16214803 PubMed] [http://nar.oxfordjournals.org/cgi/content/full/33/17/5691 NAR] [http://www.theseed.org/SubsystemPaperSupplementalMaterial/index.html Supplemental Online Material] # Angly, F.E., Felts, B., Breitbart, M., Salamon, P., Edwards, R.A., Carlson, C., Chan, A.M., Haynes, M., Kelley, S., Liu, H. et al. (2006) The marine viromes of four oceanic regions. PLoS Biol, 4. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=The%20marine%20viromes%20of%20four%20oceanic%20regions&cmd_current= PubMed] [http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pbio.0040368&ct=1 PLoS Biology] # DeLong, E.F., Preston, C.M., Mincer, T., Rich, V., Hallam, S.J., Frigaard, N.U., Martinez, A., Sullivan, M.B., Edwards, R., Brito, B.R. et al. (2006) Community genomics among stratified microbial assemblages in the ocean's interior. Science, 311, 496-503. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=Community%20genomics%20among%20stratified%20microbial%20assemblages%20in%20the%20ocean%27s%20interior&cmd_current= PubMed] # Edwards, R.A., Rodriguez-Brito, B., Wegley, L., Haynes, M., Breitbart, M., Peterson, D.M., Saar, M.O., Alexander, S., Alexander, E.C., Jr. and Rohwer, F. (2006) Using pyrosequencing to shed light on deep mine microbial ecology. BMC Genomics, 7, 57. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=16549033&cmd_current= PubMed] [http://www.biomedcentral.com/1471-2164/7/57 BioMed Central] # Krause, L., Diaz, N.N., Bartels, D., Edwards, R.A., Puhler, A., Rohwer, F., Meyer, F. and Stoye, J. (2006) Finding novel genes in bacterial communities isolated from the environment. Bioinformatics, 22, e281. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=16873483&cmd_current= PubMed] [http://bioinformatics.oxfordjournals.org/cgi/reprint/22/14/e281 NAR] # Rodriguez-Brito, B., Rohwer, F. and Edwards, R. (2006) An application of statistics to comparative metagenomics. BMC Bioinformatics, 7, 162. # El Yacoubi B, Bonnett S, Anderson JN, Swairjo MA, Iwata-Reuyl D, de Crécy-Lagard V. (2006) Discovery of a new prokaryotic type I GTP cyclohydrolase family. J Biol Chem. Dec 8;281(49):37586-93. Epub 2006 Oct 10. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17032654&cmd_current= PubMed] [http://www.jbc.org/cgi/content/full/281/49/37586 JBC]# Fierer, N., Breitbart, M., Nulton, J., Salamon, P., Lozupone, P., Jones, R., Robeson, M., Edwards, R., Felts, B., Rayhawk, S. et al. (2007) Metagenomic and small-subunit RNA surveys reveal the high genetic diversity of bacteria, archaea, fungi, and viruses in soil. Appl Environ Microbiol, 73, 7059-7066. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17827313&cmd_current= PubMed] [http://aem.asm.org/cgi/content/full/73/21/7059?view=long&pmid=17827313 AEM] # de Crecy-Lagard V, Hanson AD. (2007) Finding novel metabolic genes through plant-prokaryote phylogenomics. Trends Microbiol. Dec;15(12):563-70. Epub 2007 Nov 9. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17997099&cmd_current= PubMed] [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TD0-4R3BW70-1&_user=10&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=45c7be528111535816858125516a93ad Trends] # de Crecy-Lagard V, El Yacoubi B, de la Garza RD, Noiriel A, Hanson AD. (2007) Comparative genomics of bacterial and plant folate synthesis and salvage: predictions and validations. BMC Genomics. Jul 23;8:245.[http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17645794&cmd_current= PubMed] [http://www.biomedcentral.com/1471-2164/8/245 Biomed Central] # McNeil LK, Reich C, Aziz RK, Bartels D, Cohoon M, Disz T, Edwards RA, Gerdes SY, Hwang K, Kubal M, Margaryan GR, Meyer F, Mihalo W, Olsen GJ, Olson R, Osterman AL, Paarmann D, Paczian T, Parrello B, Pusch GD, Rodionov DA, Shi X, Vassieva O, Vonstein V, Zagnitko OP, Xia F, Zinner J, Overbeek R, Stevens R.(2007) The National Microbial Pathogen Database Resource (NMPDR): A genomics platform based on subsystem annotation. Nucleic Acids Res. 2007 Jan;35(Database issue):D347-53 [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17145713 PubMed] [http://nar.oxfordjournals.org/cgi/content/full/35/suppl_1/D347 NAR] # Wegley, L., Breitbart, M., Edwards, R. and Rohwer, F. (2007) Functional and taxonimic analysis of coral-associated microbes using metagenomic analysis. Environ Microbiol, 9, 2707-2719. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17922755&cmd_current= PubMed] [http://www.blackwell-synergy.com/doi/abs/10.1111/j.1462-2920.2007.01383.x Environ Microbiol] Yang, C., D. A. Rodionov, X. Li, O. N. Laikova, M. S. Gelfand, O. P. Zagnitko, M. F. Romine, A. Y. Obraztsova, K. H. Nealson, and A. L. Osterman. (2006). Comparative genomics and experimental characterization of N-acetylglucosamine utilization pathway of Shewanella oneidensis. J Biol Chem 281:29872-85. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=16857666 # Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S., (2006). Experimental and computational assessment of conditionally essential genes in E. coli. J Bacteriol. 188(23):8259-71. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17012394 # Gerdes, S., R. Edwards, M. Kubal, M. Fonstein, R. Stevens, and A. Osterman. (2006). Essential genes on metabolic maps. Curr Opin Biotechnol 17:448-56. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=16978855. # Osterman, A., and T. Begley. (2007). A Subsystems-based approach to the identification of drug targets in bacterial pathogens, p. 132-170. In H.Boshoff and C.Barry (ed.), Progress in Drug Research, vol. 64. Birkhauser Verlag, Basel. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17195474 # Dmitry A. Rodionov, Oleg V. Kurnasov, Boguslaw Stec, Yan Wang, Mary F. Roberts, and Andrei L. Osterman (2007) Genomic identification and in vitro reconstitution of a complete biosynthetic pathway for the osmolyte di-myo-inositol-phosphate. . Proc Natl Acad Sci U S A. Mar 13;104(11):4279-84. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17360515 # Gupta N, Tanner S, Jaitly N, Adkins JN, Lipton M, Edwards R, Romine M, Osterman A, Bafna V, Smith RD, Pevzner PA. (2007) Whole proteome analysis of post-translational modifications: Applications of mass-spectrometry for proteogenomic annotation.Genome Res. Sep;17(9):1362-77. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17690205 PubMed] [http://www.genome.org/cgi/content/full/17/9/1362 Genome Research] # JR. Yates III and AL. Osterman (2007) Introduction: advances in genomics and proteomics. Chem Rev. Aug;107(8):3363-6. Epub 2007 Jul 21. [http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/cr068201u ACS] # Yang C, Rodionov DA, Rodionova IA, Li X, Osterman AL. (2007) Glycerate 2-kinase of Thermotoga maritima and genomic reconstruction of related metabolic pathways., J Bacteriol. 2007 Dec 21; [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=18156253&cmd_current= PubMed] [http://jb.asm.org/cgi/reprint/JB.01469-07v1?view=long&pmid=18156253 JBact] ==In press== # Desnues CG, B Rodriguez-Brito, S Rayhawk, S Kelley, T Tran, M Haynes, H Liu, D Hall, FE Angly, RA Edwards, RB Thurber, P Reid, J Siefert, V Souza, DL Valentine, BK Swan, M Breitbart, F Rohwer (2008; accepted) Biodiversity and biogeography of phages in modern stromatolites and thrombolites. Nature In press. # Mou, X.S., S., Edwards, R.A., Hodson, R.E. and Moran, M.A. (2007) Generalist Species Dominate Bacterial Carbon Processing in the Coastal Ocean. Nature, In Press. # Breitbart M, M Haynes, S Kelley, F Angly, R Edwards, B Felts, JM Mahaffy, J Mueller, J Nulton, S Rayhawk, B Rodriguez-Brito, P Salamon, F Rohwer (2008) Viral diversity and dynamics in an infant's gut. 1da17fd81438095a023e3278175a3767e5390023 1779 1778 2007-12-31T21:54:17Z RobEdwards 14 wikitext text/x-wiki *2005 # Overbeek R, Begley T, Butler RM, Choudhuri JV, Chuang HY, Cohoon M, de Crécy-Lagard V, Diaz N, Disz T, Edwards R, Fonstein M, Frank ED, Gerdes S, Glass EM, Goesmann A, Hanson A, Iwata-Reuyl D, Jensen R, Jamshidi N, Krause L, Kubal M, Larsen N, Linke B, McHardy AC, Meyer F, Neuweger H, Olsen G, Olson R, Osterman A, Portnoy V, Pusch GD, Rodionov DA, Rückert C, Steiner J, Stevens R, Thiele I, Vassieva O, Ye Y, Zagnitko O, Vonstein V. (2005) Oct 7;33(17):5691-702. [http://www.ncbi.nlm.nih.gov/pubmed/16214803 PubMed] [http://nar.oxfordjournals.org/cgi/content/full/33/17/5691 NAR] [http://www.theseed.org/SubsystemPaperSupplementalMaterial/index.html Supplemental Online Material] *2006 # Angly, F.E., Felts, B., Breitbart, M., Salamon, P., Edwards, R.A., Carlson, C., Chan, A.M., Haynes, M., Kelley, S., Liu, H. et al. (2006) The marine viromes of four oceanic regions. PLoS Biol, 4. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=The%20marine%20viromes%20of%20four%20oceanic%20regions&cmd_current= PubMed] [http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pbio.0040368&ct=1 PLoS Biology] # DeLong, E.F., Preston, C.M., Mincer, T., Rich, V., Hallam, S.J., Frigaard, N.U., Martinez, A., Sullivan, M.B., Edwards, R., Brito, B.R. et al. (2006) Community genomics among stratified microbial assemblages in the ocean's interior. Science, 311, 496-503. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=Community%20genomics%20among%20stratified%20microbial%20assemblages%20in%20the%20ocean%27s%20interior&cmd_current= PubMed] # Edwards, R.A., Rodriguez-Brito, B., Wegley, L., Haynes, M., Breitbart, M., Peterson, D.M., Saar, M.O., Alexander, S., Alexander, E.C., Jr. and Rohwer, F. (2006) Using pyrosequencing to shed light on deep mine microbial ecology. BMC Genomics, 7, 57. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=16549033&cmd_current= PubMed] [http://www.biomedcentral.com/1471-2164/7/57 BioMed Central] # Gerdes, S., R. Edwards, M. Kubal, M. Fonstein, R. Stevens, and A. Osterman. (2006). Essential genes on metabolic maps. Curr Opin Biotechnol 17:448-56. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=16978855 PubMed] [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VRV-4KWTFBB-1&_user=10&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=3067cb821f4b494047d5270860f5557c Science Direct] # Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S., (2006). Experimental and computational assessment of conditionally essential genes in E. coli. J Bacteriol. 188(23):8259-71. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17012394 PubMed] [http://jb.asm.org/cgi/content/full/188/23/8259?view=long&pmid=17012394 JBact] # Krause, L., Diaz, N.N., Bartels, D., Edwards, R.A., Puhler, A., Rohwer, F., Meyer, F. and Stoye, J. (2006) Finding novel genes in bacterial communities isolated from the environment. Bioinformatics, 22, e281. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=16873483&cmd_current= PubMed] [http://bioinformatics.oxfordjournals.org/cgi/reprint/22/14/e281 NAR] # Rodriguez-Brito, B., Rohwer, F. and Edwards, R. (2006) An application of statistics to comparative metagenomics. BMC Bioinformatics, 7, 162. # El Yacoubi B, Bonnett S, Anderson JN, Swairjo MA, Iwata-Reuyl D, de Crécy-Lagard V. (2006) Discovery of a new prokaryotic type I GTP cyclohydrolase family. J Biol Chem. Dec 8;281(49):37586-93. Epub 2006 Oct 10. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17032654&cmd_current= PubMed] [http://www.jbc.org/cgi/content/full/281/49/37586 JBC]# Fierer, N., Breitbart, M., Nulton, J., Salamon, P., Lozupone, P., Jones, R., Robeson, M., Edwards, R., Felts, B., Rayhawk, S. et al. (2007) Metagenomic and small-subunit RNA surveys reveal the high genetic diversity of bacteria, archaea, fungi, and viruses in soil. Appl Environ Microbiol, 73, 7059-7066. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17827313&cmd_current= PubMed] [http://aem.asm.org/cgi/content/full/73/21/7059?view=long&pmid=17827313 AEM] # Yang, C., D. A. Rodionov, X. Li, O. N. Laikova, M. S. Gelfand, O. P. Zagnitko, M. F. Romine, A. Y. Obraztsova, K. H. Nealson, and A. L. Osterman. (2006). Comparative genomics and experimental characterization of N-acetylglucosamine utilization pathway of Shewanella oneidensis. J Biol Chem 281:29872-85. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=16857666 PubMed] [http://www.jbc.org/cgi/content/full/281/40/29872 JBC] *2007 # de Crecy-Lagard V, Hanson AD. (2007) Finding novel metabolic genes through plant-prokaryote phylogenomics. Trends Microbiol. Dec;15(12):563-70. Epub 2007 Nov 9. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17997099&cmd_current= PubMed] [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TD0-4R3BW70-1&_user=10&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=45c7be528111535816858125516a93ad Trends] # de Crecy-Lagard V, El Yacoubi B, de la Garza RD, Noiriel A, Hanson AD. (2007) Comparative genomics of bacterial and plant folate synthesis and salvage: predictions and validations. BMC Genomics. Jul 23;8:245.[http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17645794&cmd_current= PubMed] [http://www.biomedcentral.com/1471-2164/8/245 Biomed Central] # Gupta N, Tanner S, Jaitly N, Adkins JN, Lipton M, Edwards R, Romine M, Osterman A, Bafna V, Smith RD, Pevzner PA. (2007) Whole proteome analysis of post-translational modifications: Applications of mass-spectrometry for proteogenomic annotation.Genome Res. Sep;17(9):1362-77. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17690205 PubMed] [http://www.genome.org/cgi/content/full/17/9/1362 Genome Research] # McNeil LK, Reich C, Aziz RK, Bartels D, Cohoon M, Disz T, Edwards RA, Gerdes SY, Hwang K, Kubal M, Margaryan GR, Meyer F, Mihalo W, Olsen GJ, Olson R, Osterman AL, Paarmann D, Paczian T, Parrello B, Pusch GD, Rodionov DA, Shi X, Vassieva O, Vonstein V, Zagnitko OP, Xia F, Zinner J, Overbeek R, Stevens R.(2007) The National Microbial Pathogen Database Resource (NMPDR): A genomics platform based on subsystem annotation. Nucleic Acids Res. 2007 Jan;35(Database issue):D347-53 [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17145713 PubMed] [http://nar.oxfordjournals.org/cgi/content/full/35/suppl_1/D347 NAR] # Osterman, A., and T. Begley. (2007). A Subsystems-based approach to the identification of drug targets in bacterial pathogens, p. 132-170. In H.Boshoff and C.Barry (ed.), Progress in Drug Research, vol. 64. Birkhauser Verlag, Basel. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17195474 PubMed] # Dmitry A. Rodionov, Oleg V. Kurnasov, Boguslaw Stec, Yan Wang, Mary F. Roberts, and Andrei L. Osterman (2007) Genomic identification and in vitro reconstitution of a complete biosynthetic pathway for the osmolyte di-myo-inositol-phosphate. . Proc Natl Acad Sci U S A. Mar 13;104(11):4279-84. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17360515 PubMed] [http://www.pnas.org/cgi/content/full/104/11/4279 PNAS] # Wegley, L., Breitbart, M., Edwards, R. and Rohwer, F. (2007) Functional and taxonimic analysis of coral-associated microbes using metagenomic analysis. Environ Microbiol, 9, 2707-2719. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17922755&cmd_current= PubMed] [http://www.blackwell-synergy.com/doi/abs/10.1111/j.1462-2920.2007.01383.x Environ Microbiol] # Yang C, Rodionov DA, Rodionova IA, Li X, Osterman AL. (2007) Glycerate 2-kinase of Thermotoga maritima and genomic reconstruction of related metabolic pathways., J Bacteriol. 2007 Dec 21; [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=18156253&cmd_current= PubMed] [http://jb.asm.org/cgi/reprint/JB.01469-07v1?view=long&pmid=18156253 JBact] # JR. Yates III and AL. Osterman (2007) Introduction: advances in genomics and proteomics. Chem Rev. Aug;107(8):3363-6. Epub 2007 Jul 21. [http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/cr068201u ACS] ==In press== # Desnues CG, B Rodriguez-Brito, S Rayhawk, S Kelley, T Tran, M Haynes, H Liu, D Hall, FE Angly, RA Edwards, RB Thurber, P Reid, J Siefert, V Souza, DL Valentine, BK Swan, M Breitbart, F Rohwer (2008; accepted) Biodiversity and biogeography of phages in modern stromatolites and thrombolites. Nature In press. # Mou, X.S., S., Edwards, R.A., Hodson, R.E. and Moran, M.A. (2007) Generalist Species Dominate Bacterial Carbon Processing in the Coastal Ocean. Nature, In Press. # Breitbart M, M Haynes, S Kelley, F Angly, R Edwards, B Felts, JM Mahaffy, J Mueller, J Nulton, S Rayhawk, B Rodriguez-Brito, P Salamon, F Rohwer (2008) Viral diversity and dynamics in an infant's gut. 8a78f012fe0060690f339de79bbd8a3fa3257ee2 1780 1779 2007-12-31T21:54:51Z RobEdwards 14 wikitext text/x-wiki *2005 # Overbeek R, Begley T, Butler RM, Choudhuri JV, Chuang HY, Cohoon M, de Crécy-Lagard V, Diaz N, Disz T, Edwards R, Fonstein M, Frank ED, Gerdes S, Glass EM, Goesmann A, Hanson A, Iwata-Reuyl D, Jensen R, Jamshidi N, Krause L, Kubal M, Larsen N, Linke B, McHardy AC, Meyer F, Neuweger H, Olsen G, Olson R, Osterman A, Portnoy V, Pusch GD, Rodionov DA, Rückert C, Steiner J, Stevens R, Thiele I, Vassieva O, Ye Y, Zagnitko O, Vonstein V. (2005) Oct 7;33(17):5691-702. [http://www.ncbi.nlm.nih.gov/pubmed/16214803 PubMed] [http://nar.oxfordjournals.org/cgi/content/full/33/17/5691 NAR] [http://www.theseed.org/SubsystemPaperSupplementalMaterial/index.html Supplemental Online Material] *2006 # Angly, F.E., Felts, B., Breitbart, M., Salamon, P., Edwards, R.A., Carlson, C., Chan, A.M., Haynes, M., Kelley, S., Liu, H. et al. (2006) The marine viromes of four oceanic regions. PLoS Biol, 4. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=The%20marine%20viromes%20of%20four%20oceanic%20regions&cmd_current= PubMed] [http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pbio.0040368&ct=1 PLoS Biology] # DeLong, E.F., Preston, C.M., Mincer, T., Rich, V., Hallam, S.J., Frigaard, N.U., Martinez, A., Sullivan, M.B., Edwards, R., Brito, B.R. et al. (2006) Community genomics among stratified microbial assemblages in the ocean's interior. Science, 311, 496-503. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=Community%20genomics%20among%20stratified%20microbial%20assemblages%20in%20the%20ocean%27s%20interior&cmd_current= PubMed] # Edwards, R.A., Rodriguez-Brito, B., Wegley, L., Haynes, M., Breitbart, M., Peterson, D.M., Saar, M.O., Alexander, S., Alexander, E.C., Jr. and Rohwer, F. (2006) Using pyrosequencing to shed light on deep mine microbial ecology. BMC Genomics, 7, 57. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=16549033&cmd_current= PubMed] [http://www.biomedcentral.com/1471-2164/7/57 BioMed Central] # Gerdes, S., R. Edwards, M. Kubal, M. Fonstein, R. Stevens, and A. Osterman. (2006). Essential genes on metabolic maps. Curr Opin Biotechnol 17:448-56. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=16978855 PubMed] [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VRV-4KWTFBB-1&_user=10&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=3067cb821f4b494047d5270860f5557c Science Direct] # Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S., (2006). Experimental and computational assessment of conditionally essential genes in E. coli. J Bacteriol. 188(23):8259-71. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17012394 PubMed] [http://jb.asm.org/cgi/content/full/188/23/8259?view=long&pmid=17012394 JBact] # Krause, L., Diaz, N.N., Bartels, D., Edwards, R.A., Puhler, A., Rohwer, F., Meyer, F. and Stoye, J. (2006) Finding novel genes in bacterial communities isolated from the environment. Bioinformatics, 22, e281. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=16873483&cmd_current= PubMed] [http://bioinformatics.oxfordjournals.org/cgi/reprint/22/14/e281 NAR] # Rodriguez-Brito, B., Rohwer, F. and Edwards, R. (2006) An application of statistics to comparative metagenomics. BMC Bioinformatics, 7, 162. # El Yacoubi B, Bonnett S, Anderson JN, Swairjo MA, Iwata-Reuyl D, de Crécy-Lagard V. (2006) Discovery of a new prokaryotic type I GTP cyclohydrolase family. J Biol Chem. Dec 8;281(49):37586-93. Epub 2006 Oct 10. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17032654&cmd_current= PubMed] [http://www.jbc.org/cgi/content/full/281/49/37586 JBC]# Fierer, N., Breitbart, M., Nulton, J., Salamon, P., Lozupone, P., Jones, R., Robeson, M., Edwards, R., Felts, B., Rayhawk, S. et al. (2007) Metagenomic and small-subunit RNA surveys reveal the high genetic diversity of bacteria, archaea, fungi, and viruses in soil. Appl Environ Microbiol, 73, 7059-7066. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17827313&cmd_current= PubMed] [http://aem.asm.org/cgi/content/full/73/21/7059?view=long&pmid=17827313 AEM] # Yang, C., D. A. Rodionov, X. Li, O. N. Laikova, M. S. Gelfand, O. P. Zagnitko, M. F. Romine, A. Y. Obraztsova, K. H. Nealson, and A. L. Osterman. (2006). Comparative genomics and experimental characterization of N-acetylglucosamine utilization pathway of Shewanella oneidensis. J Biol Chem 281:29872-85. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=16857666 PubMed] [http://www.jbc.org/cgi/content/full/281/40/29872 JBC] *2007 # de Crecy-Lagard V, Hanson AD. (2007) Finding novel metabolic genes through plant-prokaryote phylogenomics. Trends Microbiol. Dec;15(12):563-70. Epub 2007 Nov 9. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17997099&cmd_current= PubMed] [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TD0-4R3BW70-1&_user=10&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=45c7be528111535816858125516a93ad Trends] # de Crecy-Lagard V, El Yacoubi B, de la Garza RD, Noiriel A, Hanson AD. (2007) Comparative genomics of bacterial and plant folate synthesis and salvage: predictions and validations. BMC Genomics. Jul 23;8:245.[http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17645794&cmd_current= PubMed] [http://www.biomedcentral.com/1471-2164/8/245 Biomed Central] # Gupta N, Tanner S, Jaitly N, Adkins JN, Lipton M, Edwards R, Romine M, Osterman A, Bafna V, Smith RD, Pevzner PA. (2007) Whole proteome analysis of post-translational modifications: Applications of mass-spectrometry for proteogenomic annotation.Genome Res. Sep;17(9):1362-77. 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[http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/cr068201u ACS] =In press= # Desnues CG, B Rodriguez-Brito, S Rayhawk, S Kelley, T Tran, M Haynes, H Liu, D Hall, FE Angly, RA Edwards, RB Thurber, P Reid, J Siefert, V Souza, DL Valentine, BK Swan, M Breitbart, F Rohwer (2008; accepted) Biodiversity and biogeography of phages in modern stromatolites and thrombolites. Nature In press. # Mou, X.S., S., Edwards, R.A., Hodson, R.E. and Moran, M.A. (2007) Generalist Species Dominate Bacterial Carbon Processing in the Coastal Ocean. Nature, In Press. # Breitbart M, M Haynes, S Kelley, F Angly, R Edwards, B Felts, JM Mahaffy, J Mueller, J Nulton, S Rayhawk, B Rodriguez-Brito, P Salamon, F Rohwer (2008) Viral diversity and dynamics in an infant's gut. a920796b27425c1f393df12f5bf804cd6ce165b4 1782 1781 2008-01-08T06:18:44Z RobEdwards 14 /* 2006 */ wikitext text/x-wiki =2005= # Overbeek R, Begley T, Butler RM, Choudhuri JV, Chuang HY, Cohoon M, de Crécy-Lagard V, Diaz N, Disz T, Edwards R, Fonstein M, Frank ED, Gerdes S, Glass EM, Goesmann A, Hanson A, Iwata-Reuyl D, Jensen R, Jamshidi N, Krause L, Kubal M, Larsen N, Linke B, McHardy AC, Meyer F, Neuweger H, Olsen G, Olson R, Osterman A, Portnoy V, Pusch GD, Rodionov DA, Rückert C, Steiner J, Stevens R, Thiele I, Vassieva O, Ye Y, Zagnitko O, Vonstein V. (2005) Oct 7;33(17):5691-702. 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[http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=Community%20genomics%20among%20stratified%20microbial%20assemblages%20in%20the%20ocean%27s%20interior&cmd_current= PubMed] # Edwards, R.A., Rodriguez-Brito, B., Wegley, L., Haynes, M., Breitbart, M., Peterson, D.M., Saar, M.O., Alexander, S., Alexander, E.C., Jr. and Rohwer, F. (2006) Using pyrosequencing to shed light on deep mine microbial ecology. BMC Genomics, 7, 57. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=16549033&cmd_current= PubMed] [http://www.biomedcentral.com/1471-2164/7/57 BioMed Central] # Gerdes, S., R. Edwards, M. Kubal, M. Fonstein, R. Stevens, and A. Osterman. (2006). Essential genes on metabolic maps. Curr Opin Biotechnol 17:448-56. 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Jul 23;8:245.[http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17645794&cmd_current= PubMed] [http://www.biomedcentral.com/1471-2164/8/245 Biomed Central] # Gupta N, Tanner S, Jaitly N, Adkins JN, Lipton M, Edwards R, Romine M, Osterman A, Bafna V, Smith RD, Pevzner PA. (2007) Whole proteome analysis of post-translational modifications: Applications of mass-spectrometry for proteogenomic annotation.Genome Res. Sep;17(9):1362-77. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17690205 PubMed] [http://www.genome.org/cgi/content/full/17/9/1362 Genome Research] # McNeil LK, Reich C, Aziz RK, Bartels D, Cohoon M, Disz T, Edwards RA, Gerdes SY, Hwang K, Kubal M, Margaryan GR, Meyer F, Mihalo W, Olsen GJ, Olson R, Osterman AL, Paarmann D, Paczian T, Parrello B, Pusch GD, Rodionov DA, Shi X, Vassieva O, Vonstein V, Zagnitko OP, Xia F, Zinner J, Overbeek R, Stevens R.(2007) The National Microbial Pathogen Database Resource (NMPDR): A genomics platform based on subsystem annotation. Nucleic Acids Res. 2007 Jan;35(Database issue):D347-53 [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17145713 PubMed] [http://nar.oxfordjournals.org/cgi/content/full/35/suppl_1/D347 NAR] # Osterman, A., and T. Begley. (2007). A Subsystems-based approach to the identification of drug targets in bacterial pathogens, p. 132-170. In H.Boshoff and C.Barry (ed.), Progress in Drug Research, vol. 64. Birkhauser Verlag, Basel. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17195474 PubMed] # Dmitry A. Rodionov, Oleg V. Kurnasov, Boguslaw Stec, Yan Wang, Mary F. Roberts, and Andrei L. Osterman (2007) Genomic identification and in vitro reconstitution of a complete biosynthetic pathway for the osmolyte di-myo-inositol-phosphate. . Proc Natl Acad Sci U S A. Mar 13;104(11):4279-84. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17360515 PubMed] [http://www.pnas.org/cgi/content/full/104/11/4279 PNAS] # Wegley, L., Breitbart, M., Edwards, R. and Rohwer, F. (2007) Functional and taxonimic analysis of coral-associated microbes using metagenomic analysis. Environ Microbiol, 9, 2707-2719. 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Nature, In Press. # Breitbart M, M Haynes, S Kelley, F Angly, R Edwards, B Felts, JM Mahaffy, J Mueller, J Nulton, S Rayhawk, B Rodriguez-Brito, P Salamon, F Rohwer (2008) Viral diversity and dynamics in an infant's gut. 89d323b08002535c0254dad2dc6356fcfd38b811 1801 1800 2008-04-16T13:17:23Z FolkerMeyer 2 wikitext text/x-wiki =2005= # Overbeek R, Begley T, Butler RM, Choudhuri JV, Chuang HY, Cohoon M, de Crécy-Lagard V, Diaz N, Disz T, Edwards R, Fonstein M, Frank ED, Gerdes S, Glass EM, Goesmann A, Hanson A, Iwata-Reuyl D, Jensen R, Jamshidi N, Krause L, Kubal M, Larsen N, Linke B, McHardy AC, Meyer F, Neuweger H, Olsen G, Olson R, Osterman A, Portnoy V, Pusch GD, Rodionov DA, Rückert C, Steiner J, Stevens R, Thiele I, Vassieva O, Ye Y, Zagnitko O, Vonstein V. (2005) Oct 7;33(17):5691-702. 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[http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=Community%20genomics%20among%20stratified%20microbial%20assemblages%20in%20the%20ocean%27s%20interior&cmd_current= PubMed] # Edwards, R.A., Rodriguez-Brito, B., Wegley, L., Haynes, M., Breitbart, M., Peterson, D.M., Saar, M.O., Alexander, S., Alexander, E.C., Jr. and Rohwer, F. (2006) Using pyrosequencing to shed light on deep mine microbial ecology. BMC Genomics, 7, 57. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=16549033&cmd_current= PubMed] [http://www.biomedcentral.com/1471-2164/7/57 BioMed Central] # Gerdes, S., R. Edwards, M. Kubal, M. Fonstein, R. Stevens, and A. Osterman. (2006). Essential genes on metabolic maps. Curr Opin Biotechnol 17:448-56. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=16978855 PubMed] [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VRV-4KWTFBB-1&_user=10&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=3067cb821f4b494047d5270860f5557c Science Direct] # Gerdes, S., Kurnasov, O., Shatalin, K., Polanuyer, B., Sloutsky, R., Vonstein, V., Overbeek, R., and A.L. Osterman (2006). Comparative Genomics of NAD Biosynthesis in Cyanobacteria. J. Bacteriol. 188: 3012-3023. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=16585762&cmd_current= PubMed] [http://jb.asm.org/cgi/content/abstract/188/8/3012 J. Bact] # Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S., (2006). Experimental and computational assessment of conditionally essential genes in E. coli. J Bacteriol. 188(23):8259-71. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17012394 PubMed] [http://jb.asm.org/cgi/content/full/188/23/8259?view=long&pmid=17012394 JBact] # Krause, L., Diaz, N.N., Bartels, D., Edwards, R.A., Puhler, A., Rohwer, F., Meyer, F. and Stoye, J. (2006) Finding novel genes in bacterial communities isolated from the environment. Bioinformatics, 22, e281. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=16873483&cmd_current= PubMed] [http://bioinformatics.oxfordjournals.org/cgi/reprint/22/14/e281 NAR] # Rodriguez-Brito, B., Rohwer, F. and Edwards, R. (2006) An application of statistics to comparative metagenomics. BMC Bioinformatics, 7, 162. # El Yacoubi B, Bonnett S, Anderson JN, Swairjo MA, Iwata-Reuyl D, de Crécy-Lagard V. (2006) Discovery of a new prokaryotic type I GTP cyclohydrolase family. J Biol Chem. Dec 8;281(49):37586-93. Epub 2006 Oct 10. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17032654&cmd_current= PubMed] [http://www.jbc.org/cgi/content/full/281/49/37586 JBC]# Fierer, N., Breitbart, M., Nulton, J., Salamon, P., Lozupone, P., Jones, R., Robeson, M., Edwards, R., Felts, B., Rayhawk, S. et al. (2007) Metagenomic and small-subunit RNA surveys reveal the high genetic diversity of bacteria, archaea, fungi, and viruses in soil. Appl Environ Microbiol, 73, 7059-7066. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17827313&cmd_current= PubMed] [http://aem.asm.org/cgi/content/full/73/21/7059?view=long&pmid=17827313 AEM] # Yang, C., D. A. Rodionov, X. Li, O. N. Laikova, M. S. Gelfand, O. P. Zagnitko, M. F. Romine, A. Y. Obraztsova, K. H. Nealson, and A. L. Osterman. (2006). Comparative genomics and experimental characterization of N-acetylglucosamine utilization pathway of Shewanella oneidensis. J Biol Chem 281:29872-85. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=16857666 PubMed] [http://www.jbc.org/cgi/content/full/281/40/29872 JBC] =2007= # de Crecy-Lagard V, Hanson AD. (2007) Finding novel metabolic genes through plant-prokaryote phylogenomics. Trends Microbiol. Dec;15(12):563-70. Epub 2007 Nov 9. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17997099&cmd_current= PubMed] [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TD0-4R3BW70-1&_user=10&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=45c7be528111535816858125516a93ad Trends] # de Crecy-Lagard V, El Yacoubi B, de la Garza RD, Noiriel A, Hanson AD. (2007) Comparative genomics of bacterial and plant folate synthesis and salvage: predictions and validations. BMC Genomics. Jul 23;8:245.[http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17645794&cmd_current= PubMed] [http://www.biomedcentral.com/1471-2164/8/245 Biomed Central] # Gupta N, Tanner S, Jaitly N, Adkins JN, Lipton M, Edwards R, Romine M, Osterman A, Bafna V, Smith RD, Pevzner PA. (2007) Whole proteome analysis of post-translational modifications: Applications of mass-spectrometry for proteogenomic annotation.Genome Res. Sep;17(9):1362-77. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17690205 PubMed] [http://www.genome.org/cgi/content/full/17/9/1362 Genome Research] # McNeil LK, Reich C, Aziz RK, Bartels D, Cohoon M, Disz T, Edwards RA, Gerdes SY, Hwang K, Kubal M, Margaryan GR, Meyer F, Mihalo W, Olsen GJ, Olson R, Osterman AL, Paarmann D, Paczian T, Parrello B, Pusch GD, Rodionov DA, Shi X, Vassieva O, Vonstein V, Zagnitko OP, Xia F, Zinner J, Overbeek R, Stevens R.(2007) The National Microbial Pathogen Database Resource (NMPDR): A genomics platform based on subsystem annotation. Nucleic Acids Res. 2007 Jan;35(Database issue):D347-53 [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17145713 PubMed] [http://nar.oxfordjournals.org/cgi/content/full/35/suppl_1/D347 NAR] # Osterman, A., and T. Begley. (2007). A Subsystems-based approach to the identification of drug targets in bacterial pathogens, p. 132-170. In H.Boshoff and C.Barry (ed.), Progress in Drug Research, vol. 64. Birkhauser Verlag, Basel. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17195474 PubMed] # Dmitry A. Rodionov, Oleg V. Kurnasov, Boguslaw Stec, Yan Wang, Mary F. Roberts, and Andrei L. Osterman (2007) Genomic identification and in vitro reconstitution of a complete biosynthetic pathway for the osmolyte di-myo-inositol-phosphate. . Proc Natl Acad Sci U S A. Mar 13;104(11):4279-84. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17360515 PubMed] [http://www.pnas.org/cgi/content/full/104/11/4279 PNAS] # Wegley, L., Breitbart, M., Edwards, R. and Rohwer, F. (2007) Functional and taxonimic analysis of coral-associated microbes using metagenomic analysis. Environ Microbiol, 9, 2707-2719. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17922755&cmd_current= PubMed] [http://www.blackwell-synergy.com/doi/abs/10.1111/j.1462-2920.2007.01383.x Environ Microbiol] # Yang C, Rodionov DA, Rodionova IA, Li X, Osterman AL. (2007) Glycerate 2-kinase of Thermotoga maritima and genomic reconstruction of related metabolic pathways., J Bacteriol. 2007 Dec 21; [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=18156253&cmd_current= PubMed] [http://jb.asm.org/cgi/reprint/JB.01469-07v1?view=long&pmid=18156253 JBact] # JR. Yates III and AL. Osterman (2007) Introduction: advances in genomics and proteomics. Chem Rev. Aug;107(8):3363-6. Epub 2007 Jul 21. [http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/cr068201u ACS] # DeJongh, M., Formsma, K., Boillot, P., Gould, J., Rycenga M., and Best, A. (2007) Toward the automated generation of genome-scale metabolic networks in the SEED. BMC Bioinformatics 2007 [http://www.ncbi.nlm.nih.gov/pubmed/17462086 Pubmed] [http://www.biomedcentral.com/1471-2105/8/139 BMC Bioinformatics] =2008= # Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson R, Osterman AL, Overbeek RA, McNeil LK, Paarmann D, Paczian T, Parrello B, Pusch GD, Reich C, Stevens R, Vassieva O, Vonstein V, Wilke A, Zagnitko O. The RAST Server: rapid annotations using subsystems technology. [http://www.ncbi.nlm.nih.gov/pubmed/18261238 Pubmed] [http://www.biomedcentral.com/1471-2164/9/75 BMC Genomics] =In press= # Desnues CG, B Rodriguez-Brito, S Rayhawk, S Kelley, T Tran, M Haynes, H Liu, D Hall, FE Angly, RA Edwards, RB Thurber, P Reid, J Siefert, V Souza, DL Valentine, BK Swan, M Breitbart, F Rohwer (2008; accepted) Biodiversity and biogeography of phages in modern stromatolites and thrombolites. Nature In press. # Mou, X.S., S., Edwards, R.A., Hodson, R.E. and Moran, M.A. (2007) Generalist Species Dominate Bacterial Carbon Processing in the Coastal Ocean. Nature, In Press. # Breitbart M, M Haynes, S Kelley, F Angly, R Edwards, B Felts, JM Mahaffy, J Mueller, J Nulton, S Rayhawk, B Rodriguez-Brito, P Salamon, F Rohwer (2008) Viral diversity and dynamics in an infant's gut. c681bce0d1182a0148ca02a5af1341eb39c5ae55 1802 1801 2008-04-16T13:18:12Z FolkerMeyer 2 /* 2008 */ wikitext text/x-wiki =2005= # Overbeek R, Begley T, Butler RM, Choudhuri JV, Chuang HY, Cohoon M, de Crécy-Lagard V, Diaz N, Disz T, Edwards R, Fonstein M, Frank ED, Gerdes S, Glass EM, Goesmann A, Hanson A, Iwata-Reuyl D, Jensen R, Jamshidi N, Krause L, Kubal M, Larsen N, Linke B, McHardy AC, Meyer F, Neuweger H, Olsen G, Olson R, Osterman A, Portnoy V, Pusch GD, Rodionov DA, Rückert C, Steiner J, Stevens R, Thiele I, Vassieva O, Ye Y, Zagnitko O, Vonstein V. (2005) Oct 7;33(17):5691-702. [http://www.ncbi.nlm.nih.gov/pubmed/16214803 PubMed] [http://nar.oxfordjournals.org/cgi/content/full/33/17/5691 NAR] [http://www.theseed.org/SubsystemPaperSupplementalMaterial/index.html Supplemental Online Material] =2006= # Angly, F.E., Felts, B., Breitbart, M., Salamon, P., Edwards, R.A., Carlson, C., Chan, A.M., Haynes, M., Kelley, S., Liu, H. et al. (2006) The marine viromes of four oceanic regions. PLoS Biol, 4. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=The%20marine%20viromes%20of%20four%20oceanic%20regions&cmd_current= PubMed] [http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pbio.0040368&ct=1 PLoS Biology] # DeLong, E.F., Preston, C.M., Mincer, T., Rich, V., Hallam, S.J., Frigaard, N.U., Martinez, A., Sullivan, M.B., Edwards, R., Brito, B.R. et al. (2006) Community genomics among stratified microbial assemblages in the ocean's interior. Science, 311, 496-503. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=Community%20genomics%20among%20stratified%20microbial%20assemblages%20in%20the%20ocean%27s%20interior&cmd_current= PubMed] # Edwards, R.A., Rodriguez-Brito, B., Wegley, L., Haynes, M., Breitbart, M., Peterson, D.M., Saar, M.O., Alexander, S., Alexander, E.C., Jr. and Rohwer, F. (2006) Using pyrosequencing to shed light on deep mine microbial ecology. BMC Genomics, 7, 57. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=16549033&cmd_current= PubMed] [http://www.biomedcentral.com/1471-2164/7/57 BioMed Central] # Gerdes, S., R. Edwards, M. Kubal, M. Fonstein, R. Stevens, and A. Osterman. (2006). Essential genes on metabolic maps. Curr Opin Biotechnol 17:448-56. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=16978855 PubMed] [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VRV-4KWTFBB-1&_user=10&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=3067cb821f4b494047d5270860f5557c Science Direct] # Gerdes, S., Kurnasov, O., Shatalin, K., Polanuyer, B., Sloutsky, R., Vonstein, V., Overbeek, R., and A.L. Osterman (2006). Comparative Genomics of NAD Biosynthesis in Cyanobacteria. J. Bacteriol. 188: 3012-3023. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=16585762&cmd_current= PubMed] [http://jb.asm.org/cgi/content/abstract/188/8/3012 J. Bact] # Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S., (2006). Experimental and computational assessment of conditionally essential genes in E. coli. J Bacteriol. 188(23):8259-71. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17012394 PubMed] [http://jb.asm.org/cgi/content/full/188/23/8259?view=long&pmid=17012394 JBact] # Krause, L., Diaz, N.N., Bartels, D., Edwards, R.A., Puhler, A., Rohwer, F., Meyer, F. and Stoye, J. (2006) Finding novel genes in bacterial communities isolated from the environment. Bioinformatics, 22, e281. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=16873483&cmd_current= PubMed] [http://bioinformatics.oxfordjournals.org/cgi/reprint/22/14/e281 NAR] # Rodriguez-Brito, B., Rohwer, F. and Edwards, R. (2006) An application of statistics to comparative metagenomics. BMC Bioinformatics, 7, 162. # El Yacoubi B, Bonnett S, Anderson JN, Swairjo MA, Iwata-Reuyl D, de Crécy-Lagard V. (2006) Discovery of a new prokaryotic type I GTP cyclohydrolase family. J Biol Chem. Dec 8;281(49):37586-93. Epub 2006 Oct 10. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17032654&cmd_current= PubMed] [http://www.jbc.org/cgi/content/full/281/49/37586 JBC]# Fierer, N., Breitbart, M., Nulton, J., Salamon, P., Lozupone, P., Jones, R., Robeson, M., Edwards, R., Felts, B., Rayhawk, S. et al. (2007) Metagenomic and small-subunit RNA surveys reveal the high genetic diversity of bacteria, archaea, fungi, and viruses in soil. Appl Environ Microbiol, 73, 7059-7066. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17827313&cmd_current= PubMed] [http://aem.asm.org/cgi/content/full/73/21/7059?view=long&pmid=17827313 AEM] # Yang, C., D. A. Rodionov, X. Li, O. N. Laikova, M. S. Gelfand, O. P. Zagnitko, M. F. Romine, A. Y. Obraztsova, K. H. Nealson, and A. L. Osterman. (2006). Comparative genomics and experimental characterization of N-acetylglucosamine utilization pathway of Shewanella oneidensis. J Biol Chem 281:29872-85. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=16857666 PubMed] [http://www.jbc.org/cgi/content/full/281/40/29872 JBC] =2007= # de Crecy-Lagard V, Hanson AD. (2007) Finding novel metabolic genes through plant-prokaryote phylogenomics. Trends Microbiol. Dec;15(12):563-70. Epub 2007 Nov 9. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17997099&cmd_current= PubMed] [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TD0-4R3BW70-1&_user=10&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=45c7be528111535816858125516a93ad Trends] # de Crecy-Lagard V, El Yacoubi B, de la Garza RD, Noiriel A, Hanson AD. (2007) Comparative genomics of bacterial and plant folate synthesis and salvage: predictions and validations. BMC Genomics. Jul 23;8:245.[http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17645794&cmd_current= PubMed] [http://www.biomedcentral.com/1471-2164/8/245 Biomed Central] # Gupta N, Tanner S, Jaitly N, Adkins JN, Lipton M, Edwards R, Romine M, Osterman A, Bafna V, Smith RD, Pevzner PA. (2007) Whole proteome analysis of post-translational modifications: Applications of mass-spectrometry for proteogenomic annotation.Genome Res. Sep;17(9):1362-77. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17690205 PubMed] [http://www.genome.org/cgi/content/full/17/9/1362 Genome Research] # McNeil LK, Reich C, Aziz RK, Bartels D, Cohoon M, Disz T, Edwards RA, Gerdes SY, Hwang K, Kubal M, Margaryan GR, Meyer F, Mihalo W, Olsen GJ, Olson R, Osterman AL, Paarmann D, Paczian T, Parrello B, Pusch GD, Rodionov DA, Shi X, Vassieva O, Vonstein V, Zagnitko OP, Xia F, Zinner J, Overbeek R, Stevens R.(2007) The National Microbial Pathogen Database Resource (NMPDR): A genomics platform based on subsystem annotation. Nucleic Acids Res. 2007 Jan;35(Database issue):D347-53 [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17145713 PubMed] [http://nar.oxfordjournals.org/cgi/content/full/35/suppl_1/D347 NAR] # Osterman, A., and T. Begley. (2007). A Subsystems-based approach to the identification of drug targets in bacterial pathogens, p. 132-170. In H.Boshoff and C.Barry (ed.), Progress in Drug Research, vol. 64. Birkhauser Verlag, Basel. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17195474 PubMed] # Dmitry A. Rodionov, Oleg V. Kurnasov, Boguslaw Stec, Yan Wang, Mary F. Roberts, and Andrei L. Osterman (2007) Genomic identification and in vitro reconstitution of a complete biosynthetic pathway for the osmolyte di-myo-inositol-phosphate. . Proc Natl Acad Sci U S A. Mar 13;104(11):4279-84. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17360515 PubMed] [http://www.pnas.org/cgi/content/full/104/11/4279 PNAS] # Wegley, L., Breitbart, M., Edwards, R. and Rohwer, F. (2007) Functional and taxonimic analysis of coral-associated microbes using metagenomic analysis. Environ Microbiol, 9, 2707-2719. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17922755&cmd_current= PubMed] [http://www.blackwell-synergy.com/doi/abs/10.1111/j.1462-2920.2007.01383.x Environ Microbiol] # Yang C, Rodionov DA, Rodionova IA, Li X, Osterman AL. (2007) Glycerate 2-kinase of Thermotoga maritima and genomic reconstruction of related metabolic pathways., J Bacteriol. 2007 Dec 21; [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=18156253&cmd_current= PubMed] [http://jb.asm.org/cgi/reprint/JB.01469-07v1?view=long&pmid=18156253 JBact] # JR. Yates III and AL. Osterman (2007) Introduction: advances in genomics and proteomics. Chem Rev. Aug;107(8):3363-6. Epub 2007 Jul 21. [http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/cr068201u ACS] # DeJongh, M., Formsma, K., Boillot, P., Gould, J., Rycenga M., and Best, A. (2007) Toward the automated generation of genome-scale metabolic networks in the SEED. BMC Bioinformatics 2007 [http://www.ncbi.nlm.nih.gov/pubmed/17462086 Pubmed] [http://www.biomedcentral.com/1471-2105/8/139 BMC Bioinformatics] =2008= # Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson R, Osterman AL, Overbeek RA, McNeil LK, Paarmann D, Paczian T, Parrello B, Pusch GD, Reich C, Stevens R, Vassieva O, Vonstein V, Wilke A, Zagnitko O. BMC Genomics, 2008, The RAST Server: rapid annotations using subsystems technology. [http://www.ncbi.nlm.nih.gov/pubmed/18261238 Pubmed] [http://www.biomedcentral.com/1471-2164/9/75 BMC Genomics] =In press= # Desnues CG, B Rodriguez-Brito, S Rayhawk, S Kelley, T Tran, M Haynes, H Liu, D Hall, FE Angly, RA Edwards, RB Thurber, P Reid, J Siefert, V Souza, DL Valentine, BK Swan, M Breitbart, F Rohwer (2008; accepted) Biodiversity and biogeography of phages in modern stromatolites and thrombolites. Nature In press. # Mou, X.S., S., Edwards, R.A., Hodson, R.E. and Moran, M.A. (2007) Generalist Species Dominate Bacterial Carbon Processing in the Coastal Ocean. Nature, In Press. # Breitbart M, M Haynes, S Kelley, F Angly, R Edwards, B Felts, JM Mahaffy, J Mueller, J Nulton, S Rayhawk, B Rodriguez-Brito, P Salamon, F Rohwer (2008) Viral diversity and dynamics in an infant's gut. a4cd94dc99f359ac2f37ed7f5e0d86979a7944f0 1803 1802 2008-04-16T13:18:44Z FolkerMeyer 2 /* 2008 */ wikitext text/x-wiki =2005= # Overbeek R, Begley T, Butler RM, Choudhuri JV, Chuang HY, Cohoon M, de Crécy-Lagard V, Diaz N, Disz T, Edwards R, Fonstein M, Frank ED, Gerdes S, Glass EM, Goesmann A, Hanson A, Iwata-Reuyl D, Jensen R, Jamshidi N, Krause L, Kubal M, Larsen N, Linke B, McHardy AC, Meyer F, Neuweger H, Olsen G, Olson R, Osterman A, Portnoy V, Pusch GD, Rodionov DA, Rückert C, Steiner J, Stevens R, Thiele I, Vassieva O, Ye Y, Zagnitko O, Vonstein V. (2005) Oct 7;33(17):5691-702. [http://www.ncbi.nlm.nih.gov/pubmed/16214803 PubMed] [http://nar.oxfordjournals.org/cgi/content/full/33/17/5691 NAR] [http://www.theseed.org/SubsystemPaperSupplementalMaterial/index.html Supplemental Online Material] =2006= # Angly, F.E., Felts, B., Breitbart, M., Salamon, P., Edwards, R.A., Carlson, C., Chan, A.M., Haynes, M., Kelley, S., Liu, H. et al. (2006) The marine viromes of four oceanic regions. PLoS Biol, 4. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=The%20marine%20viromes%20of%20four%20oceanic%20regions&cmd_current= PubMed] [http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pbio.0040368&ct=1 PLoS Biology] # DeLong, E.F., Preston, C.M., Mincer, T., Rich, V., Hallam, S.J., Frigaard, N.U., Martinez, A., Sullivan, M.B., Edwards, R., Brito, B.R. et al. (2006) Community genomics among stratified microbial assemblages in the ocean's interior. Science, 311, 496-503. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=Community%20genomics%20among%20stratified%20microbial%20assemblages%20in%20the%20ocean%27s%20interior&cmd_current= PubMed] # Edwards, R.A., Rodriguez-Brito, B., Wegley, L., Haynes, M., Breitbart, M., Peterson, D.M., Saar, M.O., Alexander, S., Alexander, E.C., Jr. and Rohwer, F. (2006) Using pyrosequencing to shed light on deep mine microbial ecology. BMC Genomics, 7, 57. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=16549033&cmd_current= PubMed] [http://www.biomedcentral.com/1471-2164/7/57 BioMed Central] # Gerdes, S., R. Edwards, M. Kubal, M. Fonstein, R. Stevens, and A. Osterman. (2006). Essential genes on metabolic maps. Curr Opin Biotechnol 17:448-56. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=16978855 PubMed] [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VRV-4KWTFBB-1&_user=10&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=3067cb821f4b494047d5270860f5557c Science Direct] # Gerdes, S., Kurnasov, O., Shatalin, K., Polanuyer, B., Sloutsky, R., Vonstein, V., Overbeek, R., and A.L. Osterman (2006). Comparative Genomics of NAD Biosynthesis in Cyanobacteria. J. Bacteriol. 188: 3012-3023. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=16585762&cmd_current= PubMed] [http://jb.asm.org/cgi/content/abstract/188/8/3012 J. Bact] # Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S., (2006). Experimental and computational assessment of conditionally essential genes in E. coli. J Bacteriol. 188(23):8259-71. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17012394 PubMed] [http://jb.asm.org/cgi/content/full/188/23/8259?view=long&pmid=17012394 JBact] # Krause, L., Diaz, N.N., Bartels, D., Edwards, R.A., Puhler, A., Rohwer, F., Meyer, F. and Stoye, J. (2006) Finding novel genes in bacterial communities isolated from the environment. Bioinformatics, 22, e281. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=16873483&cmd_current= PubMed] [http://bioinformatics.oxfordjournals.org/cgi/reprint/22/14/e281 NAR] # Rodriguez-Brito, B., Rohwer, F. and Edwards, R. (2006) An application of statistics to comparative metagenomics. BMC Bioinformatics, 7, 162. # El Yacoubi B, Bonnett S, Anderson JN, Swairjo MA, Iwata-Reuyl D, de Crécy-Lagard V. (2006) Discovery of a new prokaryotic type I GTP cyclohydrolase family. J Biol Chem. Dec 8;281(49):37586-93. Epub 2006 Oct 10. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17032654&cmd_current= PubMed] [http://www.jbc.org/cgi/content/full/281/49/37586 JBC]# Fierer, N., Breitbart, M., Nulton, J., Salamon, P., Lozupone, P., Jones, R., Robeson, M., Edwards, R., Felts, B., Rayhawk, S. et al. (2007) Metagenomic and small-subunit RNA surveys reveal the high genetic diversity of bacteria, archaea, fungi, and viruses in soil. Appl Environ Microbiol, 73, 7059-7066. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17827313&cmd_current= PubMed] [http://aem.asm.org/cgi/content/full/73/21/7059?view=long&pmid=17827313 AEM] # Yang, C., D. A. Rodionov, X. Li, O. N. Laikova, M. S. Gelfand, O. P. Zagnitko, M. F. Romine, A. Y. Obraztsova, K. H. Nealson, and A. L. Osterman. (2006). Comparative genomics and experimental characterization of N-acetylglucosamine utilization pathway of Shewanella oneidensis. J Biol Chem 281:29872-85. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=16857666 PubMed] [http://www.jbc.org/cgi/content/full/281/40/29872 JBC] =2007= # de Crecy-Lagard V, Hanson AD. (2007) Finding novel metabolic genes through plant-prokaryote phylogenomics. Trends Microbiol. Dec;15(12):563-70. Epub 2007 Nov 9. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17997099&cmd_current= PubMed] [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TD0-4R3BW70-1&_user=10&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=45c7be528111535816858125516a93ad Trends] # de Crecy-Lagard V, El Yacoubi B, de la Garza RD, Noiriel A, Hanson AD. (2007) Comparative genomics of bacterial and plant folate synthesis and salvage: predictions and validations. BMC Genomics. Jul 23;8:245.[http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17645794&cmd_current= PubMed] [http://www.biomedcentral.com/1471-2164/8/245 Biomed Central] # Gupta N, Tanner S, Jaitly N, Adkins JN, Lipton M, Edwards R, Romine M, Osterman A, Bafna V, Smith RD, Pevzner PA. (2007) Whole proteome analysis of post-translational modifications: Applications of mass-spectrometry for proteogenomic annotation.Genome Res. Sep;17(9):1362-77. 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In H.Boshoff and C.Barry (ed.), Progress in Drug Research, vol. 64. Birkhauser Verlag, Basel. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17195474 PubMed] # Dmitry A. Rodionov, Oleg V. Kurnasov, Boguslaw Stec, Yan Wang, Mary F. Roberts, and Andrei L. Osterman (2007) Genomic identification and in vitro reconstitution of a complete biosynthetic pathway for the osmolyte di-myo-inositol-phosphate. . Proc Natl Acad Sci U S A. Mar 13;104(11):4279-84. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17360515 PubMed] [http://www.pnas.org/cgi/content/full/104/11/4279 PNAS] # Wegley, L., Breitbart, M., Edwards, R. and Rohwer, F. (2007) Functional and taxonimic analysis of coral-associated microbes using metagenomic analysis. Environ Microbiol, 9, 2707-2719. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17922755&cmd_current= PubMed] [http://www.blackwell-synergy.com/doi/abs/10.1111/j.1462-2920.2007.01383.x Environ Microbiol] # Yang C, Rodionov DA, Rodionova IA, Li X, Osterman AL. (2007) Glycerate 2-kinase of Thermotoga maritima and genomic reconstruction of related metabolic pathways., J Bacteriol. 2007 Dec 21; [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=18156253&cmd_current= PubMed] [http://jb.asm.org/cgi/reprint/JB.01469-07v1?view=long&pmid=18156253 JBact] # JR. Yates III and AL. Osterman (2007) Introduction: advances in genomics and proteomics. Chem Rev. Aug;107(8):3363-6. Epub 2007 Jul 21. [http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/cr068201u ACS] # DeJongh, M., Formsma, K., Boillot, P., Gould, J., Rycenga M., and Best, A. (2007) Toward the automated generation of genome-scale metabolic networks in the SEED. BMC Bioinformatics 2007 [http://www.ncbi.nlm.nih.gov/pubmed/17462086 Pubmed] [http://www.biomedcentral.com/1471-2105/8/139 BMC Bioinformatics] =2008= # Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson R, Osterman AL, Overbeek RA, McNeil LK, Paarmann D, Paczian T, Parrello B, Pusch GD, Reich C, Stevens R, Vassieva O, Vonstein V, Wilke A, Zagnitko O. (2008) , The RAST Server: rapid annotations using subsystems technology. BMC Genomics [http://www.ncbi.nlm.nih.gov/pubmed/18261238 Pubmed] [http://www.biomedcentral.com/1471-2164/9/75 BMC Genomics] =In press= # Desnues CG, B Rodriguez-Brito, S Rayhawk, S Kelley, T Tran, M Haynes, H Liu, D Hall, FE Angly, RA Edwards, RB Thurber, P Reid, J Siefert, V Souza, DL Valentine, BK Swan, M Breitbart, F Rohwer (2008; accepted) Biodiversity and biogeography of phages in modern stromatolites and thrombolites. Nature In press. # Mou, X.S., S., Edwards, R.A., Hodson, R.E. and Moran, M.A. (2007) Generalist Species Dominate Bacterial Carbon Processing in the Coastal Ocean. Nature, In Press. # Breitbart M, M Haynes, S Kelley, F Angly, R Edwards, B Felts, JM Mahaffy, J Mueller, J Nulton, S Rayhawk, B Rodriguez-Brito, P Salamon, F Rohwer (2008) Viral diversity and dynamics in an infant's gut. 2778b173e2b92e66fc775c3be0ca4ddeb6e26128 1804 1803 2008-04-16T13:22:56Z FolkerMeyer 2 wikitext text/x-wiki =2005= # Overbeek R, Begley T, Butler RM, Choudhuri JV, Chuang HY, Cohoon M, de Crécy-Lagard V, Diaz N, Disz T, Edwards R, Fonstein M, Frank ED, Gerdes S, Glass EM, Goesmann A, Hanson A, Iwata-Reuyl D, Jensen R, Jamshidi N, Krause L, Kubal M, Larsen N, Linke B, McHardy AC, Meyer F, Neuweger H, Olsen G, Olson R, Osterman A, Portnoy V, Pusch GD, Rodionov DA, Rückert C, Steiner J, Stevens R, Thiele I, Vassieva O, Ye Y, Zagnitko O, Vonstein V. (2005) Oct 7;33(17):5691-702. [http://www.ncbi.nlm.nih.gov/pubmed/16214803 PubMed] [http://nar.oxfordjournals.org/cgi/content/full/33/17/5691 NAR] [http://www.theseed.org/SubsystemPaperSupplementalMaterial/index.html Supplemental Online Material] =2006= # Angly, F.E., Felts, B., Breitbart, M., Salamon, P., Edwards, R.A., Carlson, C., Chan, A.M., Haynes, M., Kelley, S., Liu, H. et al. (2006) The marine viromes of four oceanic regions. PLoS Biol, 4. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=The%20marine%20viromes%20of%20four%20oceanic%20regions&cmd_current= PubMed] [http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pbio.0040368&ct=1 PLoS Biology] # DeLong, E.F., Preston, C.M., Mincer, T., Rich, V., Hallam, S.J., Frigaard, N.U., Martinez, A., Sullivan, M.B., Edwards, R., Brito, B.R. et al. (2006) Community genomics among stratified microbial assemblages in the ocean's interior. Science, 311, 496-503. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=Community%20genomics%20among%20stratified%20microbial%20assemblages%20in%20the%20ocean%27s%20interior&cmd_current= PubMed] # Edwards, R.A., Rodriguez-Brito, B., Wegley, L., Haynes, M., Breitbart, M., Peterson, D.M., Saar, M.O., Alexander, S., Alexander, E.C., Jr. and Rohwer, F. (2006) Using pyrosequencing to shed light on deep mine microbial ecology. BMC Genomics, 7, 57. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=16549033&cmd_current= PubMed] [http://www.biomedcentral.com/1471-2164/7/57 BioMed Central] # Gerdes, S., R. Edwards, M. Kubal, M. Fonstein, R. Stevens, and A. Osterman. (2006). Essential genes on metabolic maps. Curr Opin Biotechnol 17:448-56. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=16978855 PubMed] [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VRV-4KWTFBB-1&_user=10&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=3067cb821f4b494047d5270860f5557c Science Direct] # Gerdes, S., Kurnasov, O., Shatalin, K., Polanuyer, B., Sloutsky, R., Vonstein, V., Overbeek, R., and A.L. Osterman (2006). Comparative Genomics of NAD Biosynthesis in Cyanobacteria. J. Bacteriol. 188: 3012-3023. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=16585762&cmd_current= PubMed] [http://jb.asm.org/cgi/content/abstract/188/8/3012 J. Bact] # Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S., (2006). Experimental and computational assessment of conditionally essential genes in E. coli. J Bacteriol. 188(23):8259-71. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17012394 PubMed] [http://jb.asm.org/cgi/content/full/188/23/8259?view=long&pmid=17012394 JBact] # Krause, L., Diaz, N.N., Bartels, D., Edwards, R.A., Puhler, A., Rohwer, F., Meyer, F. and Stoye, J. (2006) Finding novel genes in bacterial communities isolated from the environment. Bioinformatics, 22, e281. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=16873483&cmd_current= PubMed] [http://bioinformatics.oxfordjournals.org/cgi/reprint/22/14/e281 NAR] # Rodriguez-Brito, B., Rohwer, F. and Edwards, R. (2006) An application of statistics to comparative metagenomics. BMC Bioinformatics, 7, 162. # El Yacoubi B, Bonnett S, Anderson JN, Swairjo MA, Iwata-Reuyl D, de Crécy-Lagard V. (2006) Discovery of a new prokaryotic type I GTP cyclohydrolase family. J Biol Chem. Dec 8;281(49):37586-93. Epub 2006 Oct 10. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17032654&cmd_current= PubMed] [http://www.jbc.org/cgi/content/full/281/49/37586 JBC]# Fierer, N., Breitbart, M., Nulton, J., Salamon, P., Lozupone, P., Jones, R., Robeson, M., Edwards, R., Felts, B., Rayhawk, S. et al. (2007) Metagenomic and small-subunit RNA surveys reveal the high genetic diversity of bacteria, archaea, fungi, and viruses in soil. Appl Environ Microbiol, 73, 7059-7066. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17827313&cmd_current= PubMed] [http://aem.asm.org/cgi/content/full/73/21/7059?view=long&pmid=17827313 AEM] # Yang, C., D. A. Rodionov, X. Li, O. N. Laikova, M. S. Gelfand, O. P. Zagnitko, M. F. Romine, A. Y. Obraztsova, K. H. Nealson, and A. L. Osterman. (2006). Comparative genomics and experimental characterization of N-acetylglucosamine utilization pathway of Shewanella oneidensis. J Biol Chem 281:29872-85. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=16857666 PubMed] [http://www.jbc.org/cgi/content/full/281/40/29872 JBC] =2007= # de Crecy-Lagard V, Hanson AD. (2007) Finding novel metabolic genes through plant-prokaryote phylogenomics. Trends Microbiol. Dec;15(12):563-70. Epub 2007 Nov 9. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17997099&cmd_current= PubMed] [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TD0-4R3BW70-1&_user=10&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=45c7be528111535816858125516a93ad Trends] # de Crecy-Lagard V, El Yacoubi B, de la Garza RD, Noiriel A, Hanson AD. (2007) Comparative genomics of bacterial and plant folate synthesis and salvage: predictions and validations. BMC Genomics. Jul 23;8:245.[http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17645794&cmd_current= PubMed] [http://www.biomedcentral.com/1471-2164/8/245 Biomed Central] # Gupta N, Tanner S, Jaitly N, Adkins JN, Lipton M, Edwards R, Romine M, Osterman A, Bafna V, Smith RD, Pevzner PA. (2007) Whole proteome analysis of post-translational modifications: Applications of mass-spectrometry for proteogenomic annotation.Genome Res. Sep;17(9):1362-77. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17690205 PubMed] [http://www.genome.org/cgi/content/full/17/9/1362 Genome Research] # McNeil LK, Reich C, Aziz RK, Bartels D, Cohoon M, Disz T, Edwards RA, Gerdes SY, Hwang K, Kubal M, Margaryan GR, Meyer F, Mihalo W, Olsen GJ, Olson R, Osterman AL, Paarmann D, Paczian T, Parrello B, Pusch GD, Rodionov DA, Shi X, Vassieva O, Vonstein V, Zagnitko OP, Xia F, Zinner J, Overbeek R, Stevens R.(2007) The National Microbial Pathogen Database Resource (NMPDR): A genomics platform based on subsystem annotation. Nucleic Acids Res. 2007 Jan;35(Database issue):D347-53 [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17145713 PubMed] [http://nar.oxfordjournals.org/cgi/content/full/35/suppl_1/D347 NAR] # Osterman, A., and T. Begley. (2007). A Subsystems-based approach to the identification of drug targets in bacterial pathogens, p. 132-170. In H.Boshoff and C.Barry (ed.), Progress in Drug Research, vol. 64. Birkhauser Verlag, Basel. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17195474 PubMed] # Dmitry A. Rodionov, Oleg V. Kurnasov, Boguslaw Stec, Yan Wang, Mary F. Roberts, and Andrei L. Osterman (2007) Genomic identification and in vitro reconstitution of a complete biosynthetic pathway for the osmolyte di-myo-inositol-phosphate. . Proc Natl Acad Sci U S A. Mar 13;104(11):4279-84. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17360515 PubMed] [http://www.pnas.org/cgi/content/full/104/11/4279 PNAS] # Wegley, L., Breitbart, M., Edwards, R. and Rohwer, F. (2007) Functional and taxonimic analysis of coral-associated microbes using metagenomic analysis. Environ Microbiol, 9, 2707-2719. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17922755&cmd_current= PubMed] [http://www.blackwell-synergy.com/doi/abs/10.1111/j.1462-2920.2007.01383.x Environ Microbiol] # Yang C, Rodionov DA, Rodionova IA, Li X, Osterman AL. (2007) Glycerate 2-kinase of Thermotoga maritima and genomic reconstruction of related metabolic pathways., J Bacteriol. 2007 Dec 21; [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=18156253&cmd_current= PubMed] [http://jb.asm.org/cgi/reprint/JB.01469-07v1?view=long&pmid=18156253 JBact] # JR. Yates III and AL. Osterman (2007) Introduction: advances in genomics and proteomics. Chem Rev. Aug;107(8):3363-6. Epub 2007 Jul 21. [http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/cr068201u ACS] # DeJongh, M., Formsma, K., Boillot, P., Gould, J., Rycenga M., and Best, A. (2007) Toward the automated generation of genome-scale metabolic networks in the SEED. BMC Bioinformatics 2007 [http://www.ncbi.nlm.nih.gov/pubmed/17462086 Pubmed] [http://www.biomedcentral.com/1471-2105/8/139 BMC Bioinformatics] =2008= # Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson R, Osterman AL, Overbeek RA, McNeil LK, Paarmann D, Paczian T, Parrello B, Pusch GD, Reich C, Stevens R, Vassieva O, Vonstein V, Wilke A, Zagnitko O. (2008) , The RAST Server: rapid annotations using subsystems technology. BMC Genomics [http://www.ncbi.nlm.nih.gov/pubmed/18261238 Pubmed] [http://www.biomedcentral.com/1471-2164/9/75 BMC Genomics] # Dinsdale EA, Edwards RA, Hall D, Angly F, Breitbart M, Brulc JM, Furlan M, Desnues C, Haynes M, Li L, McDaniel L, Moran MA, Nelson KE, Nilsson C, Olson R, Paul J, Brito BR, Ruan Y, Swan BK, Stevens R, Valentine DL, Thurber RV, Wegley L, White BA, Rohwer F., (2008) Functional metagenomic profiling of nine biomes., Nature 2008 Apr 3;452(7187):629-32, [http://www.ncbi.nlm.nih.gov/pubmed/18337718 Pubmed] [http://www.nature.com/nature/journal/vaop/ncurrent/full/nature06810.html Nature] =In press= # Desnues CG, B Rodriguez-Brito, S Rayhawk, S Kelley, T Tran, M Haynes, H Liu, D Hall, FE Angly, RA Edwards, RB Thurber, P Reid, J Siefert, V Souza, DL Valentine, BK Swan, M Breitbart, F Rohwer (2008; accepted) Biodiversity and biogeography of phages in modern stromatolites and thrombolites. Nature In press. # Mou, X.S., S., Edwards, R.A., Hodson, R.E. and Moran, M.A. (2007) Generalist Species Dominate Bacterial Carbon Processing in the Coastal Ocean. Nature, In Press. # Breitbart M, M Haynes, S Kelley, F Angly, R Edwards, B Felts, JM Mahaffy, J Mueller, J Nulton, S Rayhawk, B Rodriguez-Brito, P Salamon, F Rohwer (2008) Viral diversity and dynamics in an infant's gut. 2fe9aceed6f7c9eda8701c69be36b71382ef7b67 1806 1804 2008-05-14T15:02:36Z RobEdwards 14 wikitext text/x-wiki =2005= # Overbeek R, Begley T, Butler RM, Choudhuri JV, Chuang HY, Cohoon M, de Crécy-Lagard V, Diaz N, Disz T, Edwards R, Fonstein M, Frank ED, Gerdes S, Glass EM, Goesmann A, Hanson A, Iwata-Reuyl D, Jensen R, Jamshidi N, Krause L, Kubal M, Larsen N, Linke B, McHardy AC, Meyer F, Neuweger H, Olsen G, Olson R, Osterman A, Portnoy V, Pusch GD, Rodionov DA, Rückert C, Steiner J, Stevens R, Thiele I, Vassieva O, Ye Y, Zagnitko O, Vonstein V. (2005) Oct 7;33(17):5691-702. [http://www.ncbi.nlm.nih.gov/pubmed/16214803 PubMed] [http://nar.oxfordjournals.org/cgi/content/full/33/17/5691 NAR] [http://www.theseed.org/SubsystemPaperSupplementalMaterial/index.html Supplemental Online Material] =2006= # Angly, F.E., Felts, B., Breitbart, M., Salamon, P., Edwards, R.A., Carlson, C., Chan, A.M., Haynes, M., Kelley, S., Liu, H. et al. (2006) The marine viromes of four oceanic regions. PLoS Biol, 4. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=The%20marine%20viromes%20of%20four%20oceanic%20regions&cmd_current= PubMed] [http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pbio.0040368&ct=1 PLoS Biology] # DeLong, E.F., Preston, C.M., Mincer, T., Rich, V., Hallam, S.J., Frigaard, N.U., Martinez, A., Sullivan, M.B., Edwards, R., Brito, B.R. et al. (2006) Community genomics among stratified microbial assemblages in the ocean's interior. Science, 311, 496-503. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=Community%20genomics%20among%20stratified%20microbial%20assemblages%20in%20the%20ocean%27s%20interior&cmd_current= PubMed] # Edwards, R.A., Rodriguez-Brito, B., Wegley, L., Haynes, M., Breitbart, M., Peterson, D.M., Saar, M.O., Alexander, S., Alexander, E.C., Jr. and Rohwer, F. (2006) Using pyrosequencing to shed light on deep mine microbial ecology. BMC Genomics, 7, 57. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=16549033&cmd_current= PubMed] [http://www.biomedcentral.com/1471-2164/7/57 BioMed Central] # Gerdes, S., R. Edwards, M. Kubal, M. Fonstein, R. Stevens, and A. Osterman. (2006). Essential genes on metabolic maps. Curr Opin Biotechnol 17:448-56. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=16978855 PubMed] [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VRV-4KWTFBB-1&_user=10&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=3067cb821f4b494047d5270860f5557c Science Direct] # Gerdes, S., Kurnasov, O., Shatalin, K., Polanuyer, B., Sloutsky, R., Vonstein, V., Overbeek, R., and A.L. Osterman (2006). Comparative Genomics of NAD Biosynthesis in Cyanobacteria. J. Bacteriol. 188: 3012-3023. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=16585762&cmd_current= PubMed] [http://jb.asm.org/cgi/content/abstract/188/8/3012 J. Bact] # Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S., (2006). Experimental and computational assessment of conditionally essential genes in E. coli. J Bacteriol. 188(23):8259-71. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17012394 PubMed] [http://jb.asm.org/cgi/content/full/188/23/8259?view=long&pmid=17012394 JBact] # Krause, L., Diaz, N.N., Bartels, D., Edwards, R.A., Puhler, A., Rohwer, F., Meyer, F. and Stoye, J. (2006) Finding novel genes in bacterial communities isolated from the environment. Bioinformatics, 22, e281. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=16873483&cmd_current= PubMed] [http://bioinformatics.oxfordjournals.org/cgi/reprint/22/14/e281 NAR] # Rodriguez-Brito, B., Rohwer, F. and Edwards, R. (2006) An application of statistics to comparative metagenomics. BMC Bioinformatics, 7, 162. # El Yacoubi B, Bonnett S, Anderson JN, Swairjo MA, Iwata-Reuyl D, de Crécy-Lagard V. (2006) Discovery of a new prokaryotic type I GTP cyclohydrolase family. J Biol Chem. Dec 8;281(49):37586-93. Epub 2006 Oct 10. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17032654&cmd_current= PubMed] [http://www.jbc.org/cgi/content/full/281/49/37586 JBC]# Fierer, N., Breitbart, M., Nulton, J., Salamon, P., Lozupone, P., Jones, R., Robeson, M., Edwards, R., Felts, B., Rayhawk, S. et al. (2007) Metagenomic and small-subunit RNA surveys reveal the high genetic diversity of bacteria, archaea, fungi, and viruses in soil. Appl Environ Microbiol, 73, 7059-7066. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17827313&cmd_current= PubMed] [http://aem.asm.org/cgi/content/full/73/21/7059?view=long&pmid=17827313 AEM] # Yang, C., D. A. Rodionov, X. Li, O. N. Laikova, M. S. Gelfand, O. P. Zagnitko, M. F. Romine, A. Y. Obraztsova, K. H. Nealson, and A. L. Osterman. (2006). Comparative genomics and experimental characterization of N-acetylglucosamine utilization pathway of Shewanella oneidensis. J Biol Chem 281:29872-85. 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Towards a richer description of our complete collection of genomes and metagenomes: the “Minimum Information about a Genome Sequence” (MIGS) specification. Nature Biotechnology, 26:541-547. [http://www.ncbi.nlm.nih.gov/pubmed/18464787 Pubmed] [http://www.nature.com/nbt/journal/v26/n5/abs/nbt1360.html Nature Biotech] # Frank JA, Reich CI, Sharma S, Weisbaum JS, Wilson BA, Olsen GJ. Critical evaluation of two primers commonly used for amplification of bacterial 16S rRNA genes. Appl Environ Microbiol. 2008 Apr;74(8):2461-70. [http://www.ncbi.nlm.nih.gov/pubmed/18296538 PubMed] [http://aem.asm.org/cgi/content/full/74/8/2461?view=long&pmid=18296538 AEM] =In press= # Breitbart M, M Haynes, S Kelley, F Angly, R Edwards, B Felts, JM Mahaffy, J Mueller, J Nulton, S Rayhawk, B Rodriguez-Brito, P Salamon, F Rohwer (2008) Viral diversity and dynamics in an infant's gut. 4b5c329e5af80a20ac924fac439b5f008e79f8cc 6 1451 1783 2008-01-31T15:50:36Z FolkerMeyer 2 Flow of annotations from Subsystem based curation into FIGfams and the subsequent use of those in the RAST server. wikitext text/x-wiki Flow of annotations from Subsystem based curation into FIGfams and the subsequent use of those in the RAST server. 88dde519876fc4cf549c28055cdca04c743041f8 6 1452 1784 2008-01-31T17:40:38Z FolkerMeyer 2 wikitext text/x-wiki da39a3ee5e6b4b0d3255bfef95601890afd80709 0 1 1785 1772 2008-01-31T17:49:17Z FolkerMeyer 2 wikitext text/x-wiki With the growing number of available genomes, the need for an environment to support effective comparative analysis increases. The original SEED Project was started in 2003 by the [http://thefig.info Fellowship for Interpretation of Genomes (FIG)] as a largely unfunded open source effort. Argonne National Laboratory and the University of Chicago joined the project, and now much of the activity occurs at those two institutions (as well as the University of Illinois at Urbana-Champaign, Hope college, San Diego State University, the Burnham Institute and a number of other institutions). The cooperative effort focuses on the development of the comparative genomics environment called the SEED and, more importantly, on the development of curated genomic data. [[Image:Data_lifecycle2.png|right|150p|Flow of data in the SEED.]] Curation of genomic data ([[Glossary#Annotation|annotation]]) is done via the curation of [[Glossary#Subsystem|subsystems]] by an expert annotator across many genomes, not one a gene by gene basis. This is also detailed in our [[Annotating_1000_genomes|manifesto]]. From the curated subsystems we extract a set of freely available protein families ([[Glossary#FIGfam|FIGfams]]). These FIGfams form the core component of our RAST automated annotation technology. Answering numerous requests for automatic Seed-Quality annotations for more or less complete bacterial and archaeal genomes, we have established the free [http://rast.nmpdr.org RAST-Server] (RAST=Rapid Annotation using Subsytems Technology). Using similar technology, we make the [http://metagenomics.nmpdr.org Metagenomics-RAST-Server] freely available. We also provide a [http://seed-viewer.theseed.org/ SEED-Viewer] that allows read-only access to the latest curated data sets. For users interested in editing and learning how to use the system, we provide the [http://theseed.uchicago.edu/FIG/index.cgi Trial-SEED]. We make all our software and data available for download via [ftp://ftp.theseed.org] , also see our [[DownloadPage]] page. * When using the SEED, please cite: Overbeek et al., [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16214803&query_hl=2&itool=pubmed_docsum|Nucleic Acids Res 33(17)], 2005 ([http://www.theseed.org/SubsystemPaperSupplementalMaterial/index.html Supplementary material]) * Our approaches to annotation, gene calling etc are outlined in a series of [[SOPs|Standard Operating Procedures]]. * Other [[papers that use the SEED]] 57599eec64e563779568a7ef33867b2224a59a81 1787 1785 2008-01-31T17:53:46Z FolkerMeyer 2 wikitext text/x-wiki With the growing number of available genomes, the need for an environment to support effective comparative analysis increases. The original SEED Project was started in 2003 by the [http://thefig.info Fellowship for Interpretation of Genomes (FIG)] as a largely unfunded open source effort. Argonne National Laboratory and the University of Chicago joined the project, and now much of the activity occurs at those two institutions (as well as the University of Illinois at Urbana-Champaign, Hope college, San Diego State University, the Burnham Institute and a number of other institutions). The cooperative effort focuses on the development of the comparative genomics environment called the SEED and, more importantly, on the development of curated genomic data. [[Image:Data_lifecycle3.png|frame|thumbnail|50px|Flow of data in the SEED.]] Curation of genomic data ([[Glossary#Annotation|annotation]]) is done via the curation of [[Glossary#Subsystem|subsystems]] by an expert annotator across many genomes, not one a gene by gene basis. This is also detailed in our [[Annotating_1000_genomes|manifesto]]. From the curated subsystems we extract a set of freely available protein families ([[Glossary#FIGfam|FIGfams]]). These FIGfams form the core component of our RAST automated annotation technology. Answering numerous requests for automatic Seed-Quality annotations for more or less complete bacterial and archaeal genomes, we have established the free [http://rast.nmpdr.org RAST-Server] (RAST=Rapid Annotation using Subsytems Technology). Using similar technology, we make the [http://metagenomics.nmpdr.org Metagenomics-RAST-Server] freely available. We also provide a [http://seed-viewer.theseed.org/ SEED-Viewer] that allows read-only access to the latest curated data sets. For users interested in editing and learning how to use the system, we provide the [http://theseed.uchicago.edu/FIG/index.cgi Trial-SEED]. We make all our software and data available for download via [ftp://ftp.theseed.org], also see our [[DownloadPage]] page. * When using the SEED, please cite: Overbeek et al., [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16214803&query_hl=2&itool=pubmed_docsum|Nucleic Acids Res 33(17)], 2005 ([http://www.theseed.org/SubsystemPaperSupplementalMaterial/index.html Supplementary material]) * Our approaches to annotation, gene calling etc are outlined in a series of [[SOPs|Standard Operating Procedures]]. * Other [[papers that use the SEED]] 676aa91477125bf809e0f9fffe931ace71688ab4 1788 1787 2008-01-31T17:57:35Z FolkerMeyer 2 wikitext text/x-wiki With the growing number of available genomes, the need for an environment to support effective comparative analysis increases. The original SEED Project was started in 2003 by the [http://thefig.info Fellowship for Interpretation of Genomes (FIG)] as a largely unfunded open source effort. Argonne National Laboratory and the University of Chicago joined the project, and now much of the activity occurs at those two institutions (as well as the University of Illinois at Urbana-Champaign, Hope college, San Diego State University, the Burnham Institute and a number of other institutions). The cooperative effort focuses on the development of the comparative genomics environment called the SEED and, more importantly, on the development of curated genomic data. [[Image:Data_lifecycle3.png|frame|thumbnail|50px|Flow of data in the SEED.]] Curation of genomic data ([[Glossary#Annotation|annotation]]) is done via the curation of [[Glossary#Subsystem|subsystems]] by an expert annotator across many genomes, not one a gene by gene basis. This is also detailed in our [[Annotating_1000_genomes|manifesto]]. From the curated subsystems we extract a set of freely available protein families ([[Glossary#FIGfam|FIGfams]]). These FIGfams form the core component of our RAST automated annotation technology. Answering numerous requests for automatic Seed-Quality annotations for more or less complete bacterial and archaeal genomes, we have established the free [http://rast.nmpdr.org RAST-Server] (RAST=Rapid Annotation using Subsytems Technology). Using similar technology, we make the [http://metagenomics.nmpdr.org Metagenomics-RAST-Server] freely available. We also provide a [http://seed-viewer.theseed.org/ SEED-Viewer] that allows read-only access to the latest curated data sets. For users interested in editing and learning how to use the system, we provide the [http://theseed.uchicago.edu/FIG/index.cgi Trial-SEED]. We make all our software and data available for download via [ftp://ftp.theseed.org], also see our [[DownloadPage]] page. * When using the SEED, please cite: Overbeek et al., [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16214803&query_hl=2&itool=pubmed_docsum|Nucleic Acids Res 33(17)], 2005 ([http://www.theseed.org/SubsystemPaperSupplementalMaterial/index.html Supplementary material]) * Our approaches to annotation, gene calling etc are outlined in a series of [[SOPs|Standard Operating Procedures]]. * Other [[papers that use the SEED]] a656cf8bc68a3f326a583b4c2339738720c5bf0c 1789 1788 2008-02-09T00:24:35Z FolkerMeyer 2 wikitext text/x-wiki With the growing number of available genomes, the need for an environment to support effective comparative analysis increases. The original SEED Project was started in 2003 by the [http://thefig.info Fellowship for Interpretation of Genomes (FIG)] as a largely unfunded open source effort. Argonne National Laboratory and the University of Chicago joined the project, and now much of the activity occurs at those two institutions (as well as the University of Illinois at Urbana-Champaign, Hope college, San Diego State University, the Burnham Institute and a number of other institutions). The cooperative effort focuses on the development of the comparative genomics environment called the SEED and, more importantly, on the development of curated genomic data. [[Image:Data_lifecycle3.png|frame|thumbnail|50px|Flow of data in the SEED.]] Curation of genomic data ([[Glossary#Annotation|annotation]]) is done via the curation of [[Glossary#Subsystem|subsystems]] by an expert annotator across many genomes, not one a gene by gene basis. This is also detailed in our [[Annotating_1000_genomes|manifesto]]. From the curated subsystems we extract a set of freely available protein families ([[Glossary#FIGfam|FIGfams]]). These FIGfams form the core component of our RAST automated annotation technology. Answering numerous requests for automatic Seed-Quality annotations for more or less complete bacterial and archaeal genomes, we have established the free [http://rast.nmpdr.org RAST-Server] (RAST=Rapid Annotation using Subsytems Technology). Using similar technology, we make the [http://metagenomics.nmpdr.org Metagenomics-RAST-Server] freely available. We also provide a [http://seed-viewer.theseed.org/ SEED-Viewer] that allows read-only access to the latest curated data sets. For users interested in editing and learning how to use the system, we provide the [http://theseed.uchicago.edu/FIG/index.cgi Trial-SEED]. We make all our software and data available for download via [ftp://ftp.theseed.org], also see our [[DownloadPage]] page. * We request that groups using the SEED cite: Overbeek et al., [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16214803&query_hl=2&itool=pubmed_docsum|Nucleic Acids Res 33(17)], 2005 ([http://www.theseed.org/SubsystemPaperSupplementalMaterial/index.html Supplementary material]) * We request that groups using the RAST server cite: Aziz et al., [http://www.biomedcentral.com/1471-2164/9/75| BMC Genomics], 2008 ([http://www.theseed.org/RASTPaperSupplementalMaterial/index.html Supplementary material]) * Our approaches to annotation, gene calling etc are outlined in a series of [[SOPs|Standard Operating Procedures]]. * Other [[papers that use the SEED]] ac52080a4c0043d34973ba624b8117048e980610 1791 1789 2008-02-13T03:20:00Z FolkerMeyer 2 wikitext text/x-wiki With the growing number of available genomes, the need for an environment to support effective comparative analysis increases. The original SEED Project was started in 2003 by the [http://thefig.info Fellowship for Interpretation of Genomes (FIG)] as a largely unfunded open source effort. Argonne National Laboratory and the University of Chicago joined the project, and now much of the activity occurs at those two institutions (as well as the University of Illinois at Urbana-Champaign, Hope college, San Diego State University, the Burnham Institute and a number of other institutions). The cooperative effort focuses on the development of the comparative genomics environment called the SEED and, more importantly, on the development of curated genomic data. [[Image:Data_lifecycle3.png|frame|thumbnail|50px|Flow of data in the SEED.]] Curation of genomic data ([[Glossary#Annotation|annotation]]) is done via the curation of [[Glossary#Subsystem|subsystems]] by an expert annotator across many genomes, not one a gene by gene basis. This is also detailed in our [[Annotating_1000_genomes|manifesto]]. From the curated subsystems we extract a set of freely available protein families ([[Glossary#FIGfam|FIGfams]]). These FIGfams form the core component of our RAST automated annotation technology. Answering numerous requests for automatic Seed-Quality annotations for more or less complete bacterial and archaeal genomes, we have established the free [http://rast.nmpdr.org RAST-Server] (RAST=Rapid Annotation using Subsytems Technology). Using similar technology, we make the [http://metagenomics.nmpdr.org Metagenomics-RAST-Server] freely available. We also provide a [http://seed-viewer.theseed.org/ SEED-Viewer] that allows read-only access to the latest curated data sets. For users interested in editing and learning how to use the system, we provide the [http://theseed.uchicago.edu/FIG/index.cgi Trial-SEED]. We make all our software and data available for download via [ftp://ftp.theseed.org], also see our [[DownloadPage]] page. * We request that groups using the SEED cite: Overbeek et al., [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16214803&query_hl=2&itool=pubmed_docsum|Nucleic Acids Res 33(17)], 2005 ([http://www.theseed.org/SubsystemPaperSupplementalMaterial/index.html Supplementary material]) * We request that groups using the RAST server cite: Aziz et al., [http://www.ncbi.nlm.nih.gov/pubmed/18261238?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum| BMC Genomics], 2008 ([http://www.theseed.org/RASTPaperSupplementalMaterial/index.html Supplementary material]) * Our approaches to annotation, gene calling etc are outlined in a series of [[SOPs|Standard Operating Procedures]]. * Other [[papers that use the SEED]] e44b4a1b91bad43fe3902830d7f54ab796ffad67 1792 1791 2008-02-14T19:44:34Z WilliamMihalo 3 wikitext text/x-wiki With the growing number of available genomes, the need for an environment to support effective comparative analysis increases. The original SEED Project was started in 2003 by the [http://thefig.info Fellowship for Interpretation of Genomes (FIG)] as a largely unfunded open source effort. Argonne National Laboratory and the University of Chicago joined the project, and now much of the activity occurs at those two institutions (as well as the University of Illinois at Urbana-Champaign, Hope college, San Diego State University, the Burnham Institute and a number of other institutions). The cooperative effort focuses on the development of the comparative genomics environment called the SEED and, more importantly, on the development of curated genomic data. [[Image:Data_lifecycle3.png|frame|thumbnail|50px|Flow of data in the SEED.]] Curation of genomic data ([[Glossary#Annotation|annotation]]) is done via the curation of [[Glossary#Subsystem|subsystems]] by an expert annotator across many genomes, not one a gene by gene basis. This is also detailed in our [[Annotating_1000_genomes|manifesto]]. From the curated subsystems we extract a set of freely available protein families ([[Glossary#FIGfam|FIGfams]]). These FIGfams form the core component of our RAST automated annotation technology. Answering numerous requests for automatic Seed-Quality annotations for more or less complete bacterial and archaeal genomes, we have established the free [http://rast.nmpdr.org RAST-Server] (RAST=Rapid Annotation using Subsytems Technology). Using similar technology, we make the [http://metagenomics.nmpdr.org Metagenomics-RAST-Server] freely available. We also provide a [http://seed-viewer.theseed.org/ SEED-Viewer] that allows read-only access to the latest curated data sets. For users interested in editing and learning how to use the system, we provide the [http://theseed.uchicago.edu/FIG/index.cgi Trial-SEED]. We make all our software and data available for download via [ftp://ftp.theseed.org], also see our [[DownloadPage]] page. * We request that groups using the SEED cite: Overbeek et al., [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16214803&query_hl=2&itool=pubmed_docsum|Nucleic Nucleic Acids Res 33(17)], 2005 ([http://www.theseed.org/SubsystemPaperSupplementalMaterial/index.html Supplementary material]) * We request that groups using the RAST server cite: Aziz et al., [http://www.ncbi.nlm.nih.gov/pubmed/18261238?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum| BMC Genomics], 2008 ([http://www.theseed.org/RASTPaperSupplementalMaterial/index.html Supplementary material]) * Our approaches to annotation, gene calling etc are outlined in a series of [[SOPs|Standard Operating Procedures]]. * Other [[papers that use the SEED]] eb87ff318f7cf95514bb85e72a6de4fd2a1b6bee 6 1453 1786 2008-01-31T17:52:22Z FolkerMeyer 2 wikitext text/x-wiki da39a3ee5e6b4b0d3255bfef95601890afd80709 0 1454 1790 2008-02-11T22:01:54Z DanielPaarmann 8 wikitext text/x-wiki The RAST Server offers a brief quality report on the Job Details of your genome. The purpose of this page is to explain what those statistics mean and how we compute them. For those explanations, PEG refers to protein encoding gene and is equivalent to a CDS (Coding Sequence). == Summary == '''Number of Features:''' Total number of features (PEGs + RNAs) '''Number of Warnings:''' Total number of non-fatal warning-conditions detected. '''Number of fatal problems:''' Total number of fatal error-conditions detected. The difference between warnings and fatal problems is the impact on the RAST pipeline. While both are serious quality problems found by our automated control, only fatal problems require (your) intervention, eg. running the automated correction methods provided by the RAST pipeline. Please note that you can decide to apply all available automatic corrections during the upload. '''Possibly missing genes:''' Crude but conservative estimate of the expected number of "undercalled" PEGs in the remaining gaps between features: Estimated number of potentially "missing" PEGs := (number of base-pairs in gaps longer than 2 kbp) / (1 kbp/PEG) Since the probability of a "random" gap longer than 2 kbp is less than 1 in 22000, such gaps are quite unlikely due to chance. Therefore the 2 kbp minimum gap threshold is very conservative, so the estimated number of "missing" PEGs should also be conservative. == Gene problems == '''Genes with Bad Starts:''' Non-truncated PEGs with non-ATG/GTG/TTG STARTs. These will be shown as warnings since we currently do not offer automated correction methods for them. '''Genes with Bad Stops:''' Non-truncated PEGs with non-TAA/TAG/TGA STOPs (Or whatever is appropriate for a variant genetic code). Bad STOPs should be considered fatal problems, but have been downgraded to "Warnings" as they should never occur in RAST. '''Too Short''': Number of PEGs shorter than the (default) threshold of 90 bp. Such PEGs are usually considered "lint". == Overlaps == We recognize the following classes of overlaps: '''Embedded PEGs:''' Number of PEGs completely contained within another PEG. Considered a fatal error on first pass through the corrector. The following procedure is applied to automatically correct his error: If neither PEG is in a FIGfam, the embedded PEG is eliminated. If one PEG is in a FIGfam, automated removal eliminates the PEG that is not in a FIGfam. If both PEGs are in FIGfams, the shorter PEG is removed if it is less than half the length of the longer PEG. If an embedded PEG cannot be removed because both it and the PEG it is embedded in are in FIGfams and the PEGs have comparable lengths, then this problem is downgraded to a "Warning" so that processing may still proceed. '''Bad RNA Overlaps:''' Number of PEGs that overlap an RNA by more than the (default) threshold of 20 bp. Such overlaps are considered a fatal problem and the offending PEGs are unconditionally removed when automated correction has been selected. '''Convergent overlaps:''' Number of pairs of opposite-strand PEGs oriented towards each other, such that the STOP of each PEG is inside the other PEG, the START is not inside the other PEG, and the overlap exceeds the (default) threshold of 50 bp. Such overlaps are considered "Warning" conditions, not fatal. Overlaps by less than threshold are not reported. -------> <------- '''Divergent overlaps:''' Number of pairs of opposite-strand PEGs oriented away from each other, such that the START of each PEG is inside the other PEG, the STOP is not inside the other PEG, and the overlap exceeds the (default) threshold of 150 bp. Such overlaps are considered "Warning" conditions, not fatal. Overlaps by less than threshold are not reported. <------- -------> '''Same-strand overlaps:''' Number of pairs of same-strand PEGs oriented the same direction, such that overlap by more than the (default) threshold of 120 bp. Such overlaps are considered "Warning" conditions, not fatal. (They are also a proxy for the number of frameshift errors.) -------> <------- -------> <------- In addition there is flag that should never be reported to you. But just in case... '''Impossible Overlap:''' This serves as a code development flag. It is a "This Can't Happen!" condition that should never occur; if observed, it indicates that a severe logic error may exist within the overlap detection software. e751e5c7d4edb2a92185edb9bc6ad0526476e353 1793 1790 2008-02-15T14:35:10Z Marland 16 wikitext text/x-wiki The RAST Server offers a brief quality report on the [[RAST_Tutorial#Jobs_Overview|Job Details]] of your genome. The purpose of this page is to explain what those statistics mean and how we compute them. For those explanations, PEG refers to protein encoding gene and is equivalent to a CDS (Coding Sequence). == Summary == '''Number of Features:''' Total number of features (PEGs + RNAs) '''Number of Warnings:''' Total number of non-fatal warning-conditions detected*. '''Number of fatal problems:''' Total number of fatal error-conditions detected*. <nowiki>*</nowiki>The difference between warnings and fatal problems is the impact on the RAST pipeline. While both are serious quality problems found by our automated control, only fatal problems require (your) intervention, eg. running the automated correction methods provided by the RAST pipeline. Please note that you can decide to apply all available automatic corrections during the upload. Below you will find detailed explanations of these warnings and errors. '''Possibly missing genes:''' Crude but conservative estimate of the expected number of "undercalled" PEGs in the remaining gaps between features: Estimated number of potentially "missing" PEGs := (number of base-pairs in gaps longer than 2 kbp) / (1 kbp/PEG) Since the probability of a "random" gap longer than 2 kbp is less than 1 in 22000, such gaps are quite unlikely due to chance. Therefore the 2 kbp minimum gap threshold is very conservative, so the estimated number of "missing" PEGs should also be conservative. == Gene problems == '''Genes with Bad Starts:''' Non-truncated PEGs with non-ATG/GTG/TTG STARTs. These will be shown as warnings since we currently do not offer automated correction methods for them. '''Genes with Bad Stops:''' Non-truncated PEGs with non-TAA/TAG/TGA STOPs (Or whatever is appropriate for a variant genetic code). Bad STOPs should be considered fatal problems, but have been downgraded to "Warnings" as they should never occur in RAST. '''Too Short''': Number of PEGs shorter than the (default) threshold of 90 bp. Such PEGs are usually considered "lint". == Overlaps == We recognize the following classes of overlaps: '''Embedded PEGs:''' Number of PEGs completely contained within another PEG. Considered a fatal error on first pass through the corrector. The following procedure is applied to automatically correct his error: If neither PEG is in a FIGfam, the embedded PEG is eliminated. If one PEG is in a FIGfam, automated removal eliminates the PEG that is not in a FIGfam. If both PEGs are in FIGfams, the shorter PEG is removed if it is less than half the length of the longer PEG. If an embedded PEG cannot be removed because both it and the PEG it is embedded in are in FIGfams and the PEGs have comparable lengths, then this problem is downgraded to a "Warning" so that processing may still proceed. '''Bad RNA Overlaps:''' Number of PEGs that overlap an RNA by more than the (default) threshold of 20 bp. Such overlaps are considered a fatal problem and the offending PEGs are unconditionally removed when automated correction has been selected. '''Convergent overlaps:''' Number of pairs of opposite-strand PEGs oriented towards each other, such that the STOP of each PEG is inside the other PEG, the START is not inside the other PEG, and the overlap exceeds the (default) threshold of 50 bp. Such overlaps are considered "Warning" conditions, not fatal. Overlaps by less than threshold are not reported. -------> <------- '''Divergent overlaps:''' Number of pairs of opposite-strand PEGs oriented away from each other, such that the START of each PEG is inside the other PEG, the STOP is not inside the other PEG, and the overlap exceeds the (default) threshold of 150 bp. Such overlaps are considered "Warning" conditions, not fatal. Overlaps by less than threshold are not reported. <------- -------> '''Same-strand overlaps:''' Number of pairs of same-strand PEGs oriented the same direction, such that overlap by more than the (default) threshold of 120 bp. Such overlaps are considered "Warning" conditions, not fatal. (They are also a proxy for the number of frameshift errors.) -------> <------- -------> <------- In addition there is flag that should never be reported to you. But just in case... '''Impossible Overlap:''' This serves as a code development flag. It is a "This Can't Happen!" condition that should never occur; if observed, it indicates that a severe logic error may exist within the overlap detection software. 581e36be15c753ad3435909a58f6a38d0ac74d28 1794 1793 2008-02-15T17:04:41Z DanielPaarmann 8 wikitext text/x-wiki The RAST Server offers a brief quality report on the [[RAST_Tutorial#Job_Details|Job Details]] of your genome. The purpose of this page is to explain what those statistics mean and how we compute them. For those explanations, PEG refers to protein encoding gene and is equivalent to a CDS (Coding Sequence). == Summary == '''Number of Features:''' Total number of features (PEGs + RNAs) '''Number of Warnings:''' Total number of non-fatal warning-conditions detected*. '''Number of fatal problems:''' Total number of fatal error-conditions detected*. <nowiki>*</nowiki>The difference between warnings and fatal problems is the impact on the RAST pipeline. While both are serious quality problems found by our automated control, only fatal problems require (your) intervention, eg. running the automated correction methods provided by the RAST pipeline. Please note that you can decide to apply all available automatic corrections during the upload. Below you will find detailed explanations of these warnings and errors. '''Possibly missing genes:''' Crude but conservative estimate of the expected number of "undercalled" PEGs in the remaining gaps between features: Estimated number of potentially "missing" PEGs := (number of base-pairs in gaps longer than 2 kbp) / (1 kbp/PEG) Since the probability of a "random" gap longer than 2 kbp is less than 1 in 22000, such gaps are quite unlikely due to chance. Therefore the 2 kbp minimum gap threshold is very conservative, so the estimated number of "missing" PEGs should also be conservative. == Gene problems == '''Genes with Bad Starts:''' Non-truncated PEGs with non-ATG/GTG/TTG STARTs. These will be shown as warnings since we currently do not offer automated correction methods for them. '''Genes with Bad Stops:''' Non-truncated PEGs with non-TAA/TAG/TGA STOPs (Or whatever is appropriate for a variant genetic code). Bad STOPs should be considered fatal problems, but have been downgraded to "Warnings" as they should never occur in RAST. '''Too Short''': Number of PEGs shorter than the (default) threshold of 90 bp. Such PEGs are usually considered "lint". == Overlaps == We recognize the following classes of overlaps: '''Embedded PEGs:''' Number of PEGs completely contained within another PEG. Considered a fatal error on first pass through the corrector. The following procedure is applied to automatically correct his error: If neither PEG is in a FIGfam, the embedded PEG is eliminated. If one PEG is in a FIGfam, automated removal eliminates the PEG that is not in a FIGfam. If both PEGs are in FIGfams, the shorter PEG is removed if it is less than half the length of the longer PEG. If an embedded PEG cannot be removed because both it and the PEG it is embedded in are in FIGfams and the PEGs have comparable lengths, then this problem is downgraded to a "Warning" so that processing may still proceed. '''Bad RNA Overlaps:''' Number of PEGs that overlap an RNA by more than the (default) threshold of 20 bp. Such overlaps are considered a fatal problem and the offending PEGs are unconditionally removed when automated correction has been selected. '''Convergent overlaps:''' Number of pairs of opposite-strand PEGs oriented towards each other, such that the STOP of each PEG is inside the other PEG, the START is not inside the other PEG, and the overlap exceeds the (default) threshold of 50 bp. Such overlaps are considered "Warning" conditions, not fatal. Overlaps by less than threshold are not reported. -------> <------- '''Divergent overlaps:''' Number of pairs of opposite-strand PEGs oriented away from each other, such that the START of each PEG is inside the other PEG, the STOP is not inside the other PEG, and the overlap exceeds the (default) threshold of 150 bp. Such overlaps are considered "Warning" conditions, not fatal. Overlaps by less than threshold are not reported. <------- -------> '''Same-strand overlaps:''' Number of pairs of same-strand PEGs oriented the same direction, such that overlap by more than the (default) threshold of 120 bp. Such overlaps are considered "Warning" conditions, not fatal. (They are also a proxy for the number of frameshift errors.) -------> <------- -------> <------- In addition there is flag that should never be reported to you. But just in case... '''Impossible Overlap:''' This serves as a code development flag. It is a "This Can't Happen!" condition that should never occur; if observed, it indicates that a severe logic error may exist within the overlap detection software. ddce5a7897b7a2bcda3bac363723f571beeac086 0 1455 1795 2008-02-15T17:55:20Z DanielPaarmann 8 wikitext text/x-wiki The RAST service provides the following download formats for your genome: GTF GFF3 GenBank EMBL EC numbers stripped Genome Directory 3f1b8cb06bc42b482eec8a8c6467d855f962ac2f 0 1433 1796 1771 2008-03-24T02:05:15Z RobEdwards 14 wikitext text/x-wiki ===Overview=== The metagenomics RAST server (http://metagenomics.nmpdr.org) is a SEED-based environment that allows users to upload metagenomes for automated analyses. The server is built as a modified version of the RAST server. The RAST (Rapid Annotation using Subsystem Technology) technology was originally implemented to allow automated high-quality annotation of complete or draft microbial genomes using SEED data, and has been adapted for metagenome analysis. Our freely available server provides the annotation of sequence fragments, their phylogenetic classification, functional classification of samples, and comparison between multiple metagenomes. The server also computes an initial metabolic reconstruction for the metagenome and allows comparison of metabolic reconstructions of metagenomes and genomes. User submission and analysis are confidential. Although we do not guarantee a maximum turnover time, the current average processing time is about 24 hours. Currently the server handles 454 and Sanger sequence data. Data sets supplied by 454 can be uploaded directly. In either case, the data needs to be in [[Valid fasta format]]. For more information, please see [[Which Sequences Should I Upload, and Where]]. For the metagenomics service please also read this explanation of [[metagenomics sequence formats]]. The server relies on the technology and data established by FIG and the NMPDR team at Argonne National Laboratory and the University of Chicago. In addition to SEED data we use the following ribosomal RNA databases for our analyses: [http://greengenes.lbl.gov/cgi-bin/nph-index.cgi greengenes], [http://rdp.cme.msu.edu/ RDP-II] and [http://bioinformatics.psb.ugent.be/webtools/rRNA/ European ribosomal RNA database]. ===Registration=== Registration is required for metagenome submission and viewing of results. This enables us to contact users once the computation is finished and in case the users intervention is required. At the bottom of the main page is a like for registration (see Figure 1). [[Image:mg-rast-main-page.jpeg]] Required fields for registration include first and last name and your valid email address. Login information and other communication regarding the status of your metagenome analysis job(s) will be sent to the email address you provide. Optional information includes your organization and any notes you would like to send the rast server support team. Please note that your login and password are valid for use in both the MG-RAST and RAST servers. ===Submitting a Job=== Once you have registered and logged into the server, you will be directed to your Jobs Overview. At the top of this page will be a link labeled "Upload Genome" which will allow you to start a new job. Your metagenome file(s) should be uploaded as either a single plain text file containing all the sequences in FASTA format, or a gzip compressed tar archive (tar.gz) that has your FASTA sequences. Please do not upload uncompressed files larger than 30 MB. If your data set is larger, use the compressed format or contact us for other options. If you would like, you can also include the quality files in your archive. The fasta file names should end either *.fna, *.fa, or *.fasta, and the quality files should be named *.qual. The quality files are not currently used in the analysis, but the sequences will be renamed and renumbered along with the fasta sequences. If you have trouble with the upload format please email mg-rast@mcs.anl.gov and we'll be happy to help. ''Data entered into the server will not be used for any purposes or integrated into the main SEED environment, it will remain on this server for 120 days or until deleted by the submitting user.'' An email will be sent once the automatic annotation has finished or in case user intervention is required. ===Viewing Results=== The overall status of your metagenome analyses can be viewed from the main portion of the Jobs Overview page. This contains information regarding a user’s personal jobs and when applicable, jobs of the user’s organization. Information includes each job/metagenome and its status and contains information including job number, name of the user who started the job, metagenome name, and annotation progress. The table of jobs can be sorted on any column containing textual information. When the user has numerous metagenomes to select from, they can use the text boxes in the table header to search and refine the list of jobs. Clicking on the bars for a given job in the annotation progress column directs the user to the “Job Details” page where the detailed job status and access to the metagenome analysis can be found ("Browse annotated genome in SEED Viewer"). Users can also download the results in compressed GenBank format. ===MetaGenome Overview=== The MetaGenome Overview provides the user with various statistics regarding their metagenome and details on how each of these numbers are calculated can be found [[MG-RAST_Numbers|here]]. [[Image:MG-RAST-sample-overview.png]] Users can search for a given function, subsystem or process in the table, or browse the Subsystem Overview. At the top right hand side of the page is a set of tabs that offer a wide set of information to browse, explore, compare and download. Browse allows users to look through the features of this metagenome either graphically or through a table. Both allow quick navigation and filtering for features of your interest. Each feature is linked to its own detail page. Explore allows users to view scenarios. Scenarios are isolated metabolic divisions that in aggregate represent the metabolic functionality of the metagenome. Each scenario is tested for reaction availability against the annotated functions. They provide the foundation for generating a metabolic reconstruction. Comparison of two metagenomes is also possible via the compare tab. You can also export all information about this metagenome (e.g. annotations, scenarios, subsystems) into a variety of formats (e.g. EMBL, Excel) for further analysis on your own system. ==16S Sequences== The metagenomics-RAST is primarily designed to handle random community genomes. At the moment, we only provide rudimentary support for 16S DNA sequence analysis, although this is near the very top of our to-do list. Our colleagues at San Diego State University have developed two different tools for handling 16S rDNA sequences. FastGroup, a stand-alone java application ([http://www.ncbi.nlm.nih.gov/pubmed/11707150?ordinalpos=2&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Seguritan V and Rohwer F. (2001) FastGroup: a program to dereplicate libraries of 16S rDNA sequences]. BMC Bioinformatics. 2:9. Epub 2001 Oct 16.) is the original program, and it was updated to FastGroupII ([http://www.ncbi.nlm.nih.gov/pubmed/16464253?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Yu Y, Breitbart M, McNairnie P, and Rohwer F. (2006) FastGroupII: a web-based bioinformatics platform for analyses of large 16S rDNA libraries]. BMC Bioinformatics. Feb 7;7:57.). We have provided some [[instructions for using FastGroupII with large data sets]]. 20959568497ae63338115d2e678690917b74c325 1799 1796 2008-03-24T02:17:21Z RobEdwards 14 wikitext text/x-wiki ===Overview=== The metagenomics RAST server (http://metagenomics.nmpdr.org) is a SEED-based environment that allows users to upload metagenomes for automated analyses. The server is built as a modified version of the RAST server. The RAST (Rapid Annotation using Subsystem Technology) technology was originally implemented to allow automated high-quality annotation of complete or draft microbial genomes using SEED data, and has been adapted for metagenome analysis. Our freely available server provides the annotation of sequence fragments, their phylogenetic classification, functional classification of samples, and comparison between multiple metagenomes. The server also computes an initial metabolic reconstruction for the metagenome and allows comparison of metabolic reconstructions of metagenomes and genomes. User submission and analysis are confidential. Although we do not guarantee a maximum turnover time, the current average processing time is about 24 hours. Currently the server handles 454 and Sanger sequence data. Data sets supplied by 454 can be uploaded directly. In either case, the data needs to be in [[Valid fasta format]]. For more information, please see [[Which Sequences Should I Upload, and Where]]. For the metagenomics service please also read this explanation of [[metagenomics sequence formats]]. The server relies on the technology and data established by FIG and the NMPDR team at Argonne National Laboratory and the University of Chicago. In addition to SEED data we use the following ribosomal RNA databases for our analyses: [http://greengenes.lbl.gov/cgi-bin/nph-index.cgi greengenes], [http://rdp.cme.msu.edu/ RDP-II] and [http://bioinformatics.psb.ugent.be/webtools/rRNA/ European ribosomal RNA database]. ===Registration=== Registration is required for metagenome submission and viewing of results. This enables us to contact users once the computation is finished and in case the users intervention is required. At the bottom of the main page is a like for registration (see Figure 1). [[Image:mg-rast-main-page.jpeg]] Required fields for registration include first and last name and your valid email address. Login information and other communication regarding the status of your metagenome analysis job(s) will be sent to the email address you provide. Optional information includes your organization and any notes you would like to send the rast server support team. Please note that your login and password are valid for use in both the MG-RAST and RAST servers. ===Submitting a Job=== Once you have registered and logged into the server, you will be directed to your Jobs Overview. At the top of this page will be a link labeled "Upload Genome" which will allow you to start a new job. Your metagenome file(s) should be uploaded as either a single plain text file containing all the sequences in FASTA format, or a gzip compressed tar archive (tar.gz) that has your FASTA sequences. Please do not upload uncompressed files larger than 30 MB. If your data set is larger, use the compressed format or contact us for other options. If you would like, you can also include the quality files in your archive. The fasta file names should end either *.fna, *.fa, or *.fasta, and the quality files should be named *.qual. The quality files are not currently used in the analysis, but the sequences will be renamed and renumbered along with the fasta sequences. If you have trouble with the upload format please email mg-rast@mcs.anl.gov and we'll be happy to help. ''Data entered into the server will not be used for any purposes or integrated into the main SEED environment, it will remain on this server for 120 days or until deleted by the submitting user.'' An email will be sent once the automatic annotation has finished or in case user intervention is required. ===Viewing Results=== The overall status of your metagenome analyses can be viewed from the main portion of the Jobs Overview page. This contains information regarding a user’s personal jobs and when applicable, jobs of the user’s organization. Information includes each job/metagenome and its status and contains information including job number, name of the user who started the job, metagenome name, and annotation progress. The table of jobs can be sorted on any column containing textual information. When the user has numerous metagenomes to select from, they can use the text boxes in the table header to search and refine the list of jobs. Clicking on the bars for a given job in the annotation progress column directs the user to the “Job Details” page where the detailed job status and access to the metagenome analysis can be found ("Browse annotated genome in SEED Viewer"). Users can also download the results in compressed GenBank format. ===MetaGenome Overview=== The MetaGenome Overview provides the user with various statistics regarding their metagenome and details on how each of these numbers are calculated can be found [[MG-RAST_Numbers|here]]. [[Image:MG-RAST-sample-overview.png]] Users can search for a given function, subsystem or process in the table, or browse the Subsystem Overview. At the top right hand side of the page is a set of tabs that offer a wide set of information to browse, explore, compare and download. Browse allows users to look through the features of this metagenome either graphically or through a table. Both allow quick navigation and filtering for features of your interest. Each feature is linked to its own detail page. Explore allows users to view scenarios. Scenarios are isolated metabolic divisions that in aggregate represent the metabolic functionality of the metagenome. Each scenario is tested for reaction availability against the annotated functions. They provide the foundation for generating a metabolic reconstruction. Comparison of two metagenomes is also possible via the compare tab. You can also export all information about this metagenome (e.g. annotations, scenarios, subsystems) into a variety of formats (e.g. EMBL, Excel) for further analysis on your own system. ==16S Sequences== The metagenomics-RAST is primarily designed to handle random community genomes. At the moment, we only provide rudimentary support for 16S DNA sequence analysis, although this is near the very top of our to-do list. Our colleagues at San Diego State University have developed two different tools for handling 16S rDNA sequences. FastGroup, a stand-alone java application ([http://www.ncbi.nlm.nih.gov/pubmed/11707150?ordinalpos=2&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Seguritan V and Rohwer F. (2001) FastGroup: a program to dereplicate libraries of 16S rDNA sequences]. BMC Bioinformatics. 2:9. Epub 2001 Oct 16.) is the original program, and it was updated to FastGroupII ([http://www.ncbi.nlm.nih.gov/pubmed/16464253?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Yu Y, Breitbart M, McNairnie P, and Rohwer F. (2006) FastGroupII: a web-based bioinformatics platform for analyses of large 16S rDNA libraries]. BMC Bioinformatics. Feb 7;7:57.). We have provided some [[instructions for using FastGroupII with large data sets]]. We recommend FastGroupII for clustering and primary analysis of 16S libraries, and then the data from that can be fed into RDP Classifier and other programs. 0c2bb44fd50ca89317ee98d37193ebd7bf5c0d4f 0 1456 1797 2008-03-24T02:15:39Z RobEdwards 14 wikitext text/x-wiki = URL = [http://biome.sdsu.edu/fastgroup/] = Overview = The FastGroup and FastGroupII programs were written by [http://phage.sdsu.edu Forest Rohwer]'s group at [http://www.sdsu.edu/ San Diego State University]. These programs were really written and tested on small 16S data sets typically from Sanger Sequencing. However, as is often the case, they work well for larger datasets like a single 454 run focussing on 16S genes. FastGroup uses different clustering algorithms to generate both Richness (Chao1) and Diversity (Shannon-Wiener index) measures, as well as returning information about the groups and the statistics. = Tips = * I recommend removing the trimming options (by unchecking the boxes) unless you have a specific sequence you want to trim to. * '''Please do not request the rarefaction curves''' These are computationally very expensive, and will take a long time to compute on large data sets. * For Mac users, the calculation may take some time to compute and return. I recommend using firefox rather than safari. The latter times out after a few minutes whereas firefox keeps waiting. * If you have problems with this site, please email the mg-rast mailing list. Although we do not control FastGroupII, we know the developers and will work with them. We are particularly concerned not to direct too much load on their server while we figure out a solution compatible with the mg-rast. f017b7094bdfc1e447f5f01b0ad0b03fbc594ffe 1798 1797 2008-03-24T02:15:55Z RobEdwards 14 wikitext text/x-wiki = URL = [http://biome.sdsu.edu/fastgroup/ http://biome.sdsu.edu/fastgroup/] = Overview = The FastGroup and FastGroupII programs were written by [http://phage.sdsu.edu Forest Rohwer]'s group at [http://www.sdsu.edu/ San Diego State University]. These programs were really written and tested on small 16S data sets typically from Sanger Sequencing. However, as is often the case, they work well for larger datasets like a single 454 run focussing on 16S genes. FastGroup uses different clustering algorithms to generate both Richness (Chao1) and Diversity (Shannon-Wiener index) measures, as well as returning information about the groups and the statistics. = Tips = * I recommend removing the trimming options (by unchecking the boxes) unless you have a specific sequence you want to trim to. * '''Please do not request the rarefaction curves''' These are computationally very expensive, and will take a long time to compute on large data sets. * For Mac users, the calculation may take some time to compute and return. I recommend using firefox rather than safari. The latter times out after a few minutes whereas firefox keeps waiting. * If you have problems with this site, please email the mg-rast mailing list. Although we do not control FastGroupII, we know the developers and will work with them. We are particularly concerned not to direct too much load on their server while we figure out a solution compatible with the mg-rast. 5702a064059cdf221cad0604fb2f7fb272974d3d 0 1457 1805 2008-04-30T21:32:36Z Arodri7 22 wikitext text/x-wiki The purpose of the Seedviewer Evidence page is to show all protein and gene sequence related data that supports the annotations given to a FIG sequence. ---- <H2>'''Visual Protein Evidence Tab'''</H2> Information on this page is a visual of the Localization, domain structure and similarities to the query protein sequence. <br><br> <H2>'''Tabular Protein Evidence Tab'''</H2> Same information as in the visual protein evidence tab but in tables. This allows the user to view additional information about the similar sequences. <br><br><br> <H2>Explanation of "Region in ..." Colors</H2> In the protein similarities table, the table cells that describe the sequence regions responsible for the similarity are colored to reflect the extent and location of the similarity. The coloring is intended to provide a quick visual cue as to the nature of the similarity, and help in assessing broad classes of possible relationships (most particularly, whether there are reasons to doubt that these sequences have the same function). <P> The intensity (saturation) of the color depends on the fraction of the sequence that is covered by the similarity. <BLOCKQUOTE> If the similarity extends over at least 90% of the sequence, then the table cell background is white. <P> If the similarity covers less than 90% of the sequence, then there is a background color. The shorter the region of similarity, the more intense the color. </BLOCKQUOTE> <BR> The color (hue) of the cell depends of which region of the sequence is similar. <BLOCKQUOTE> The colors go from red through green to blue as the region of matching moves from the beginning to the end of the sequence. <P> The color is determined by the center of the matching region, so long matches will always have greenish hues. This might be changed in the future to give clearer indication of the position of long matches. </BLOCKQUOTE> <BR> Taken together, the colors of the subject sequence (left column) and the query sequence (right column) tell a story. <BLOCKQUOTE> <TABLE Border> <TR><TH>Subject<br>color</TH><TH>Query<br>color</TH><TH>Some possible interpretations</TH></TR> <TR><TD>White</TD><TD>White</TD><TD>Both sequences match over (essentially) their full length.</TD></TR> <TR><TD>White</TD><TD>Colored</TD><TD>The subject sequence is shorter than the query sequence. The subject sequence might be a fragment of a protein (perhaps the result of a sequencing error, or running off the end of a contig). Alternatively, the query sequence might be a multifunctional protein, and the subject sequence does not have all of the functions. A related situation is when proteins found as one peptide in some organisms are found in two separate peptides in others.</TD></TR> <TR><TD>Colored</TD><TD>White</TD><TD>The query sequence is shorter than the subject sequence. The query sequence might be a fragment of a protein (perhaps the result of a sequencing error, or running off the end of a contig). Alternatively, the subject sequence might be a multifunctional protein, and the query sequence does not have all of the functions. A related situation is when proteins found as one peptide in some organisms are found in two separate peptides in others.</TD></TR> <TR><TD>Colored</TD><TD>Same color</TD><TD>The query and subject are of similar lengths, <B>and</B> the region of similarity is the same in both sequences. This often happens when analyzing sequences that are distantly related, or when some part(s) of the molecule diverge particularly quickly.</TD></TR> <TR><TD>Colored</TD><TD>Different color</TD><TD>This happens when comparing two partial sequences that cover different parts of a molecule. Alternatively, the similarity could be due to a conserved motif shared by two molecules of quite different function.</TD></TR> </TABLE> </BLOCKQUOTE <BR> Final thoughts: <P> In considering whether two proteins have the same function, one would prefer that the similarity cover essentially the entirety of both molecules (little or no color). When this is not true, one would prefer that the colors match as closely as possible. <h2>An Explanation of the SEED Evidence Codes</h2> Within the SEED, we use evidence codes to reflect significant factors that go into making assignments of function. Some of these codes are computed and reflect information that we consider particularly useful. Others are used to reflect experimental evidence of function. <h3>icw(n): in cluster with</h3> This code indicates that the PEG occurs in a cluster with <i>n</i> other genes from the same subsystem (very strong evidence). There may be several of these for a PEG (up to one for each subsystem the PEG occurs in). <h3>isu: in subsystem unique -- the only entry in a subsystem cell</h3> This code indicates that the PEG occurs in a subsystem, and it is the only PEG for that genome that has been assigned the functional role (i.e., the cell in the spreadsheet contains a single entry). This means that, if you wish to change an annotation, you should discuss it with the owner of the subsystem. <h3>idu(n): in subsystem duplicates</h3> This code indicates that the PEG occurs in a subsystem, but it is in a cell of the spreadsheet containing duplicates (and it is not clustered with other genes connected to the same subsystem). In this case, you may make a change without notifying the owner of the subsystem, since you are probably disambiguating the situation to his benefit. <h3>ff: in FIGfam</h3> This code indicates that the protein-encoding gene is included in a FIGfam. <h3>cwn: Clustered with Nonhypothetical</h3> This code indicates that the protein-encoding gene is functionally coupled to at least one other protein that has been assigned a function that is considered "nonhypothetical". The functional coupling score must be 5 or more for this code to apply. This means that the gene co-occurs on the chromosome in at least 5 instances of genomes that are not close strains with another gene that is considered nonhypothetical. <h3>cwh: Clustered with Hypothetical</h3> This code indicates that the protein-encoding gene is functionally coupled to at least one other protein that has been assigned a function, but none that is considered "nonhypothetical". The functional coupling score must be 5 or more for this code to apply. This means that the gene co-occurs on the chromosome in at least 5 instances of genomes that are not close strains with at least one other gene, but none that is considered nonhypothetical. <h3> dlit: Direct Literature References to the Gene Exist </h3> This code is used to indicate that at least one paper (that is a "nongenome paper" in the sense that it does not reference hundreds of genes) is associated with this gene. <h3> ilit: Indirect Literature References to the Gene Exist </h3> This code is used to indicate that at least one paper (that is a "nongenome paper" in the sense that it does not reference hundreds of genes) is associated with a gene assigned the same functional role, but none to this gene itself (as far as we know). <H2>Explanation of "Function" Colors in Similarities Table</H2> The functions in the similarities table are color-coded to help find assignments that are identical to that of the query, and also the most common alternative functions. <P> <TABLE Border> <TR><TH>Meaning of each background color</TH></TR> <TR><TD bgcolor="#FFFFFF">Same function as query</TD><TR> <TR><TD bgcolor="#EECCAA">Most common other function</TD><TR> <TR><TD bgcolor="#FFAAAA">Second most common other function</TD><TR> <TR><TD bgcolor="#FFCC66">Third most common other function</TD><TR> <TR><TD bgcolor="#FFFF00">Fourth most common other function</TD><TR> <TR><TD bgcolor="#AAFFAA">Fifth most common other function</TD><TR> <TR><TD bgcolor="#BBBBFF">Sixth most common other function</TD><TR> <TR><TD bgcolor="#FFAAFF">Seventh most common other function</TD><TR> <TR><TD bgcolor="#DDDDDD">Other function</TD><TR> </TABLE> <P> When two or more functions are equally frequent, their ranking (and hence order of colors) relative to one-another is arbitrary. 9e0ea87e94ae8f20d35f007140d843b8c3f4029f 0 1436 1811 1728 2008-05-14T21:58:01Z RobEdwards 14 wikitext text/x-wiki One of the most frequent errors with uploading the data is incorrect file format. We recommend fasta format for all the sequence data to be uploaded. In particular, please check the following things: # There should be no spaces or tabs at the start or ends of the lines # The identifier line should begin with a greater than sign ">", and only one line is allowed # Typically most bioinformatics applications use the first word after the > as the identifier for the sequence. Its nice (but not essential) if this is unique # In the sequence lines (not header lines), spaces and numbers are removed. Examples of valid fasta >sequenceid gatgcagcatgcagctagcagcgacggactac... >1 this is a sequence that i know something about gatgcagcatgcagctagcagcgacggactac... Examples of invalid fasta >sequenceid This is a comment about the sequence gatgcagcatgcagctagcagcgacggactac... ''Pleae don't include comments in the sequence data'' >sequenceid gatgcagcatgcagctagcagcgacggactac... ''please don't have spaces before the > in the identifier'' >sequenceid\rgatgcagcatgcagctagcagcgacggactac... ''this is a sequence that has been edited in a mac. We try to fix them, because we're mac users too, but can't always. Please make sure you save using newlines (sometimes called UNIX format) if you are using a mac". fasta is probably the most common sequence format because it is relatively compact, and very easy to parse. There is more information about the fasta format at: # [http://en.wikipedia.org/wiki/Fasta_format Wikipedia] # [http://www.ncbi.nlm.nih.gov/blast/fasta.shtml NCBI] 8fc5574715272df06925adffa56587686f08adf5 1812 1811 2008-05-14T21:58:35Z RobEdwards 14 wikitext text/x-wiki One of the most frequent errors with uploading the data is incorrect file format. We recommend fasta format for all the sequence data to be uploaded. In particular, please check the following things: # There should be no spaces or tabs at the start or ends of the lines # The identifier line should begin with a greater than sign ">", and only one line is allowed # Typically most bioinformatics applications use the first word after the > as the identifier for the sequence. Its nice (but not essential) if this is unique # In the sequence lines (not header lines), spaces and numbers are removed. Examples of valid fasta >sequenceid gatgcagcatgcagctagcagcgacggactac... >1 this is a sequence that i know something about gatgcagcatgcagctagcagcgacggactac... Examples of invalid fasta >sequenceid This is a comment about the sequence gatgcagcatgcagctagcagcgacggactac... ''Pleae don't include comments in the sequence data'' >sequenceid gatgcagcatgcagctagcagcgacggactac... ''please don't have spaces before the > in the identifier'' >sequenceid\rgatgcagcatgcagctagcagcgacggactac... ''this is a sequence that has been edited in a mac. We try to fix them, because we're mac users too, but can't always. Please make sure you save using UNIX format if you are using a mac". fasta is probably the most common sequence format because it is relatively compact, and very easy to parse. There is more information about the fasta format at: # [http://en.wikipedia.org/wiki/Fasta_format Wikipedia] # [http://www.ncbi.nlm.nih.gov/blast/fasta.shtml NCBI] 3386da064a62b4bc0d7ee36f137cb6a575c8ad8a 1813 1812 2008-05-14T21:59:04Z RobEdwards 14 wikitext text/x-wiki One of the most frequent errors with uploading the data is incorrect file format. We recommend fasta format for all the sequence data to be uploaded. In particular, please check the following things: # There should be no spaces or tabs at the start or ends of the lines # The identifier line should begin with a greater than sign ">", and only one line is allowed # Typically most bioinformatics applications use the first word after the > as the identifier for the sequence. Its nice (but not essential) if this is unique # In the sequence lines (not header lines), spaces and numbers are removed. Examples of valid fasta >sequenceid gatgcagcatgcagctagcagcgacggactac... >1 this is a sequence that i know something about gatgcagcatgcagctagcagcgacggactac... Examples of invalid fasta >sequenceid This is a comment about the sequence gatgcagcatgcagctagcagcgacggactac... ''Pleae don't include comments in the sequence data'' >sequenceid gatgcagcatgcagctagcagcgacggactac... ''please don't have spaces before the > in the identifier'' >sequenceid\rgatgcagcatgcagctagcagcgacggactac... ''this is a sequence that has been edited in a mac.'' ''We try to fix them, because we're mac users too, but can't always.'' ''Please make sure you save using UNIX format if you are using a mac". fasta is probably the most common sequence format because it is relatively compact, and very easy to parse. There is more information about the fasta format at: # [http://en.wikipedia.org/wiki/Fasta_format Wikipedia] # [http://www.ncbi.nlm.nih.gov/blast/fasta.shtml NCBI] 8b3b2bd46b7a4e32a2ec827fa6aa15394b2df9a8 1814 1813 2008-05-14T21:59:21Z RobEdwards 14 wikitext text/x-wiki One of the most frequent errors with uploading the data is incorrect file format. We recommend fasta format for all the sequence data to be uploaded. In particular, please check the following things: # There should be no spaces or tabs at the start or ends of the lines # The identifier line should begin with a greater than sign ">", and only one line is allowed # Typically most bioinformatics applications use the first word after the > as the identifier for the sequence. Its nice (but not essential) if this is unique # In the sequence lines (not header lines), spaces and numbers are removed. Examples of valid fasta >sequenceid gatgcagcatgcagctagcagcgacggactac... >1 this is a sequence that i know something about gatgcagcatgcagctagcagcgacggactac... Examples of invalid fasta >sequenceid This is a comment about the sequence gatgcagcatgcagctagcagcgacggactac... ''Pleae don't include comments in the sequence data'' >sequenceid gatgcagcatgcagctagcagcgacggactac... ''please don't have spaces before the > in the identifier'' >sequenceid\rgatgcagcatgcagctagcagcgacggactac... ''This is a sequence that has been edited in a mac.'' ''We try to fix them, because we're mac users too, but can't always.'' ''Please make sure you save using UNIX format if you are using a mac". fasta is probably the most common sequence format because it is relatively compact, and very easy to parse. There is more information about the fasta format at: # [http://en.wikipedia.org/wiki/Fasta_format Wikipedia] # [http://www.ncbi.nlm.nih.gov/blast/fasta.shtml NCBI] f2f3a75f6fbe0251377e8adfa239778607c901e6 0 1458 1815 2008-06-20T15:53:30Z FolkerMeyer 2 wikitext text/x-wiki == MG-RAST v2.0 Homepage == === What is MG-RAST === MG-RAST (Metagenome Rapid Annotation using Subsystem Technology) is a fully-automated service for annotating metagenome samples. It is the only service that we are aware of that will handle both short reads (notably reads of 109 or 230 basepairs from a [http://en.wikipedia.org/wiki/454_life_sciences#Technology 454] instrument) and longer [http://en.wikipedia.org/wiki/DNA_sequencing#Chain-termination_methods Sanger] reads or even assembled short contigs. In the MG-RAST analysis the fragments in a given sample will be compared to protein, RNA and subsystem databases. === Overview === The MG-RAST system will utilize data structures and software generated in the context of [http://www.theseed.org The SEED] and [http://www.nmpdr.org NMPDR] to provide annotation of sequence fragments, their phylogenetic classification and an initial metabolic reconstruction. The service also provides means for comparing phylogenetic classifications and metabolic reconstructions of metagenomes. The service is built as a modified version of the [http://rast.nmpdr.org RAST] server, which was originally designed to support high-quality annotation of complete or draft microbial genomes. We have adapted this technology for the analysis of metagenomes. In addition to SEED data we use the following ribosomal RNA databases for our analyses: GREENGENES, RDP-II, SILVA, and European ribosomal RNA database. User submission and analysis are confidential, although each user may optionally allow a collaborative environment that enables multiple users to share datasets. In addition, users can also allow public access and request long-term storage of their metagenomic samples on the server. The server provides unique IDs for metagenomes and the sequences they contain and provides a stable mechanism for linking to. All data and analysis are available for download in a variety of different formats. To be able to contact you once the computation is finished and in case user intervention is required, we request that users register with email address. === What's new? (Changes from MG-RAST v1.2 to MG-RAST v2.0) === === Standard Compliance === === - Page Overview === [this will be a simple graphical overview of the pages and their links] === Manual for MG-RAST v2.0 === === Tutorial (Using MG-RAST-v2.0 to analyze my metagenome sample) === === FAQ - Contact 25fcb2654ad5a7f1e88d298bfe9cd24a3fbbfe52 1816 1815 2008-06-20T16:18:15Z FolkerMeyer 2 wikitext text/x-wiki == MG-RAST v2.0 Homepage == === What is MG-RAST === MG-RAST (Metagenome Rapid Annotation using Subsystem Technology) is a fully-automated service for annotating metagenome samples. It is the only service that we are aware of that will handle both short reads (notably reads of 109 or 230 basepairs from a [http://en.wikipedia.org/wiki/454_life_sciences#Technology 454] instrument) and longer [http://en.wikipedia.org/wiki/DNA_sequencing#Chain-termination_methods Sanger] reads or even assembled short contigs. In the MG-RAST analysis the fragments in a given sample will be compared to protein, RNA and subsystem databases. === Overview === The MG-RAST system will utilize data structures and software generated in the context of [http://www.theseed.org The SEED] and [http://www.nmpdr.org NMPDR] to provide annotation of sequence fragments, their phylogenetic classification and an initial metabolic reconstruction. The service also provides means for comparing phylogenetic classifications and metabolic reconstructions of metagenomes. The service is built as a modified version of the [http://rast.nmpdr.org RAST] server, which was originally designed to support high-quality annotation of complete or draft microbial genomes. We have adapted this technology for the analysis of metagenomes. In addition to SEED data we use the following ribosomal RNA databases for our analyses: GREENGENES, RDP-II, SILVA, and European ribosomal RNA database. User submission and analysis are confidential, although each user may optionally allow a collaborative environment that enables multiple users to share datasets. In addition, users can also allow public access and request long-term storage of their metagenomic samples on the server. The server provides unique IDs for metagenomes and the sequences they contain and provides a stable mechanism for linking to. All data and analysis are available for download in a variety of different formats. To be able to contact you once the computation is finished and in case user intervention is required, we request that users register with email address. === What's new? (Changes from MG-RAST v1.2 to MG-RAST v2.0) === We have gone through several rounds of feedback with users of version 1.2 (Many thanks to all who send suggestions!) and have included the following new capabilities in version 2.0: * The ability to download subsets of fragments as fasta (eg. all fragments matching a given [http://www.theseed.org/wiki/Glossary#Subsystem subsystem] or [http://www.theseed.org/wiki/Glossary#Functional_role functional role] * The ability to modify parameters for sequence comparison underlying both metabolic reconstruction and phylogenetic reconstruction on the fly. * The same capability for the heatmap style comparisons of both metabolisms and phylogenetic reconstructions. * We have added a recruitment plot feature, plotting fragments against microbial genomes. * The ability to use [http://www.genome.ad.jp/kegg/kegg2.html KEGG] maps map explore and compare metabolic reconstructions on several hierarchy levels (e.g. the high level metabolism overview). * We have changed the pipeline that computes the underlying data so all numbers/percentages/comparisons/etc. will have changed if you look at your data in v2.0 * We have also updated the underlying databases. Most notably the [http://www.theseed.org SEED] NR no longer from represents the status from 2006, we have added the [http://www.arb-silva.de/ Silva RNA database]) * support for groups and inviting friends to look at data * much faster user interface * ability to see/download fragments and see blast alignments * many small detailed fixes === Databases used === === Standard Compliance === === - Page Overview === [this will be a simple graphical overview of the pages and their links] === Manual for MG-RAST v2.0 === === Tutorial (Using MG-RAST-v2.0 to analyze my metagenome sample) === === Availability=== MG-RAST is open source. While we currently do not provide a defined release, current snapshots of the system are available via CVS. === FAQ - Contact 4e22a1eba13129631284b449049cb97ec1846702 1817 1816 2008-06-20T17:00:48Z FolkerMeyer 2 wikitext text/x-wiki == MG-RAST v2.0 Homepage == === What is MG-RAST === MG-RAST (Metagenome Rapid Annotation using Subsystem Technology) is a fully-automated service for annotating metagenome samples. It is the only service that we are aware of that will handle both short reads (notably reads of 109 or 230 basepairs from a [http://en.wikipedia.org/wiki/454_life_sciences#Technology 454] instrument) and longer [http://en.wikipedia.org/wiki/DNA_sequencing#Chain-termination_methods Sanger] reads or even assembled short contigs. In the MG-RAST analysis the fragments in a given sample will be compared to protein, RNA and subsystem databases. === Overview === The MG-RAST system will utilize data structures and software generated in the context of [http://www.theseed.org The SEED] and [http://www.nmpdr.org NMPDR] to provide annotation of sequence fragments, their phylogenetic classification and an initial metabolic reconstruction. The service also provides means for comparing phylogenetic classifications and metabolic reconstructions of metagenomes. The service is built as a modified version of the [http://rast.nmpdr.org RAST] server, which was originally designed to support high-quality annotation of complete or draft microbial genomes. We have adapted this technology for the analysis of metagenomes. In addition to SEED data we use the following ribosomal RNA databases for our analyses: GREENGENES, RDP-II, SILVA, and European ribosomal RNA database. User submission and analysis are confidential, although each user may optionally allow a collaborative environment that enables multiple users to share datasets. In addition, users can also allow public access and request long-term storage of their metagenomic samples on the server. The server provides unique IDs for metagenomes and the sequences they contain and provides a stable mechanism for linking to. All data and analysis are available for download in a variety of different formats. To be able to contact you once the computation is finished and in case user intervention is required, we request that users register with email address. === What's new? (Changes from MG-RAST v1.2 to MG-RAST v2.0) === We have gone through several rounds of feedback with users of version 1.2 (Many thanks to all who send suggestions!) and have included the following new capabilities in version 2.0: * Significant improvements of user interface responsiveness and overall performance. * ability to see/download fragments and see blast alignments * The ability to download subsets of fragments as fasta (eg. all fragments matching a given [http://www.theseed.org/wiki/Glossary#Subsystem subsystem] or [http://www.theseed.org/wiki/Glossary#Functional_role functional role]). * The ability to modify parameters for sequence comparison underlying both metabolic reconstruction and phylogenetic reconstruction on the fly. * The same capability for the heatmap style comparisons of both metabolisms and phylogenetic reconstructions. * We have added a recruitment plot feature, plotting fragments against microbial genomes. * The ability to use [http://www.genome.ad.jp/kegg/kegg2.html KEGG] maps map explore and compare metabolic reconstructions on several hierarchy levels (e.g. the high level metabolism overview). * We have changed the pipeline that computes the underlying data so all numbers/percentages/comparisons/etc. will have changed if you look at your data in v2.0 * We have also updated the underlying databases. Most notably the [http://www.theseed.org SEED] NR no longer from represents the status from 2006, we have added the [http://www.arb-silva.de/ Silva RNA database]) * Invite a friend feature to share data that you submitted with other users by just entering their email addresses. * Support for user driven creation and maintenance of groups. * many small detailed fixes === Databases used === * [http://www.theseed.org SEED non redundant protein database] * [http://greengenes.lbl.gov/ GREENGENES] * [3 RDP-II] * [http://www.arb-silva.de/ SILVA] === Standard Compliance === === - Page Overview === [this will be a simple graphical overview of the pages and their links] === Manual for MG-RAST v2.0 === === Tutorial (Using MG-RAST-v2.0 to analyze my metagenome sample) === === Availability=== MG-RAST is open source. While we currently do not provide a defined release, current snapshots of the system are available via CVS. === FAQ - Contact e03b52c1bc320eb584a8941a92172359c4b855df 1818 1817 2008-06-20T17:06:55Z FolkerMeyer 2 wikitext text/x-wiki == MG-RAST v2.0 Homepage == === What is MG-RAST === MG-RAST (Metagenome Rapid Annotation using Subsystem Technology) is a fully-automated service for annotating metagenome samples. It is the only service that we are aware of that will handle both short reads (notably reads of 109 or 230 basepairs from a [http://en.wikipedia.org/wiki/454_life_sciences#Technology 454] instrument) and longer [http://en.wikipedia.org/wiki/DNA_sequencing#Chain-termination_methods Sanger] reads or even assembled short contigs. In the MG-RAST analysis the fragments in a given sample will be compared to protein, RNA and subsystem databases. === Overview === The MG-RAST system will utilize data structures and software generated in the context of [http://www.theseed.org The SEED] and [http://www.nmpdr.org NMPDR] to provide annotation of sequence fragments, their phylogenetic classification and an initial metabolic reconstruction. The service also provides means for comparing phylogenetic classifications and metabolic reconstructions of metagenomes. The service is built as a modified version of the [http://rast.nmpdr.org RAST] server, which was originally designed to support high-quality annotation of complete or draft microbial genomes. We have adapted this technology for the analysis of metagenomes. In addition to SEED data we use the following ribosomal RNA databases for our analyses: GREENGENES, RDP-II, SILVA, and European ribosomal RNA database. User submission and analysis are confidential, although each user may optionally allow a collaborative environment that enables multiple users to share datasets. In addition, users can also allow public access and request long-term storage of their metagenomic samples on the server. The server provides unique IDs for metagenomes and the sequences they contain and provides a stable mechanism for linking to. All data and analysis are available for download in a variety of different formats. To be able to contact you once the computation is finished and in case user intervention is required, we request that users register with email address. === What's new? (Changes from MG-RAST v1.2 to MG-RAST v2.0) === We have gone through several rounds of feedback with users of version 1.2 (Many thanks to all who send suggestions!) and have included the following new capabilities in version 2.0: * Significant improvements of user interface responsiveness and overall performance. * ability to see/download fragments and see blast alignments * The ability to download subsets of fragments as fasta (eg. all fragments matching a given [http://www.theseed.org/wiki/Glossary#Subsystem subsystem] or [http://www.theseed.org/wiki/Glossary#Functional_role functional role]). * The ability to modify parameters for sequence comparison underlying both metabolic reconstruction and phylogenetic reconstruction on the fly. * The same capability for the heatmap style comparisons of both metabolisms and phylogenetic reconstructions. * We have added a recruitment plot feature, plotting fragments against microbial genomes. * The ability to use [http://www.genome.ad.jp/kegg/kegg2.html KEGG] maps map explore and compare metabolic reconstructions on several hierarchy levels (e.g. the high level metabolism overview). * We have changed the pipeline that computes the underlying data so all numbers/percentages/comparisons/etc. will have changed if you look at your data in v2.0 * We have also updated the underlying databases. Most notably the [http://www.theseed.org SEED] NR no longer from represents the status from 2006, we have added the [http://www.arb-silva.de/ Silva RNA database]) * Invite a friend feature to share data that you submitted with other users by just entering their email addresses. * Support for user driven creation and maintenance of groups. * many small detailed fixes === Databases used === * [http://www.theseed.org SEED non redundant protein database] * [http://greengenes.lbl.gov/ GREENGENES] * [http://rdp.cme.msu.edu/ RDP-II] * [http://www.arb-silva.de/ SILVA] === Standard Compliance === We are currently working with Dawn Fields and Renzo Kottmann from the GSC to support a version of "ANDREAS PLEASE SUPPLY THIS INFO" === - Page Overview === [this will be a simple graphical overview of the pages and their links] === Manual for MG-RAST v2.0 === === Tutorial (Using MG-RAST-v2.0 to analyze my metagenome sample) === === Availability=== MG-RAST is open source. While we currently do not provide a defined release, current snapshots of the system are available via CVS. === FAQ - Contact fa1f6566330b1c6e1b23cb0e0b0f8065aeebacf4 1819 1818 2008-06-20T17:14:50Z FolkerMeyer 2 wikitext text/x-wiki == MG-RAST v2.0 Homepage == === What is MG-RAST === MG-RAST (Metagenome Rapid Annotation using Subsystem Technology) is a fully-automated service for annotating metagenome samples. It is the only service that we are aware of that will handle both short reads (notably reads of 109 or 230 basepairs from a [http://en.wikipedia.org/wiki/454_life_sciences#Technology 454] instrument) and longer [http://en.wikipedia.org/wiki/DNA_sequencing#Chain-termination_methods Sanger] reads or even assembled short contigs. In the MG-RAST analysis the fragments in a given sample will be compared to protein, RNA and subsystem databases. === Overview === The MG-RAST system will utilize data structures and software generated in the context of [http://www.theseed.org The SEED] and [http://www.nmpdr.org NMPDR] to provide annotation of sequence fragments, their phylogenetic classification and an initial metabolic reconstruction. The service also provides means for comparing phylogenetic classifications and metabolic reconstructions of metagenomes. The service is built as a modified version of the [http://rast.nmpdr.org RAST] server, which was originally designed to support high-quality annotation of complete or draft microbial genomes. We have adapted this technology for the analysis of metagenomes. In addition to SEED data we use the following ribosomal RNA databases for our analyses: GREENGENES, RDP-II, SILVA, and European ribosomal RNA database. User submission and analysis are confidential, although each user may optionally allow a collaborative environment that enables multiple users to share datasets. In addition, users can also allow public access and request long-term storage of their metagenomic samples on the server. The server provides unique IDs for metagenomes and the sequences they contain and provides a stable mechanism for linking to. All data and analysis are available for download in a variety of different formats. To be able to contact you once the computation is finished and in case user intervention is required, we request that users register with email address. === What's new? (Changes from MG-RAST v1.2 to MG-RAST v2.0) === We have gone through several rounds of feedback with users of version 1.2 (Many thanks to all who send suggestions!) and have included the following new capabilities in version 2.0: * Significant improvements of user interface responsiveness and overall performance. * The ability to <strong>"publish" metagenomes on the MG-RAST server</strong> for public use. * The ability to <strong>download subsets</strong> of fragments as fasta (eg. all fragments matching a given eg. a [http://www.theseed.org/wiki/Glossary#Subsystem subsystem] or a [http://www.theseed.org/wiki/Glossary#Functional_role functional role]). * The ability to modify parameters for sequence comparison underlying both metabolic reconstruction and phylogenetic reconstruction on the fly. * The same capability for the heatmap style comparisons of both metabolisms and phylogenetic reconstructions. * We have added a recruitment plot feature, plotting fragments against microbial genomes. * We have added the ability to view all BLAST hits for a fragment and show the individual BLAST alignments. * The ability to use [http://www.genome.ad.jp/kegg/kegg2.html KEGG] maps map explore and compare metabolic reconstructions on several hierarchy levels (e.g. the high level metabolism overview). * We have changed the pipeline that computes the underlying data so all numbers/percentages/comparisons/etc. will have changed if you look at your data in v2.0 * We have also updated the underlying databases. Most notably the [http://www.theseed.org SEED] NR no longer from represents the status from 2006, we have added the [http://www.arb-silva.de/ Silva RNA database]) * Added the <strong>Invite a friend feature</strong> to share data that you submitted with other users by just entering their email addresses. * Support for user driven creation and maintenance of groups. * Many small detailed fixes and improvements. == Databases used == * [http://www.theseed.org SEED non redundant protein database] * [http://greengenes.lbl.gov/ GREENGENES] * [http://rdp.cme.msu.edu/ RDP-II] * [http://www.arb-silva.de/ SILVA] == Standard Compliance == We are currently working with Dawn Fields and Renzo Kottmann from the GSC to support a version of "ANDREAS PLEASE SUPPLY THIS INFO" == - Page Overview == [this will be a simple graphical overview of the pages and their links] == Manual for MG-RAST v2.0 == Separate page == Tutorial (Using MG-RAST-v2.0 to analyze my metagenome sample) == Separate page == Availability== Using MG-RAST is free for all users. We provide privacy for the data submitted and MG-RAST is open source. While we currently do not provide a defined release, current snapshots of the system are available via CVS. === FAQ - Contact d4d9061ed6df326246b1676c45b01491971ed61f 1820 1819 2008-06-20T17:18:02Z FolkerMeyer 2 wikitext text/x-wiki == MG-RAST v2.0 Homepage == === What is MG-RAST ( Executive Summary) === MG-RAST (Metagenome Rapid Annotation using Subsystem Technology) is a fully-automated service for annotating metagenome samples. It is the only service that we are aware of that will handle both short reads (notably reads of 109 or 230 basepairs from a [http://en.wikipedia.org/wiki/454_life_sciences#Technology 454] instrument) and longer [http://en.wikipedia.org/wiki/DNA_sequencing#Chain-termination_methods Sanger] reads or even assembled short contigs. In the MG-RAST analysis the fragments in a given sample will be compared to protein, RNA and subsystem databases. Both the submitted data and the MG-RAST analysis can be shared with other users or "published" to the public on the server, we provide stable unique identifiers for public metagenomes. === Overview === The MG-RAST system will utilize data structures and software generated in the context of [http://www.theseed.org The SEED] and [http://www.nmpdr.org NMPDR] to provide annotation of sequence fragments, their phylogenetic classification and an initial metabolic reconstruction. The service also provides means for comparing phylogenetic classifications and metabolic reconstructions of metagenomes. The service is built as a modified version of the [http://rast.nmpdr.org RAST] server, which was originally designed to support high-quality annotation of complete or draft microbial genomes. We have adapted this technology for the analysis of metagenomes. In addition to SEED data we use the following ribosomal RNA databases for our analyses: GREENGENES, RDP-II, SILVA, and European ribosomal RNA database. User submission and analysis are confidential, although each user may optionally allow a collaborative environment that enables multiple users to share datasets. In addition, users can also allow public access and request long-term storage of their metagenomic samples on the server. The server provides unique IDs for metagenomes and the sequences they contain and provides a stable mechanism for linking to. All data and analysis are available for download in a variety of different formats. To be able to contact you once the computation is finished and in case user intervention is required, we request that users register with email address. === What's new? (Changes from MG-RAST v1.2 to MG-RAST v2.0) === We have gone through several rounds of feedback with users of version 1.2 (Many thanks to all who send suggestions!) and have included the following new capabilities in version 2.0: * Significant improvements of user interface responsiveness and overall performance. * The ability to <strong>"publish" metagenomes on the MG-RAST server</strong> for public use. * The ability to <strong>download subsets</strong> of fragments as fasta (eg. all fragments matching a given eg. a [http://www.theseed.org/wiki/Glossary#Subsystem subsystem] or a [http://www.theseed.org/wiki/Glossary#Functional_role functional role]). * The ability to modify parameters for sequence comparison underlying both metabolic reconstruction and phylogenetic reconstruction on the fly. * The same capability for the heatmap style comparisons of both metabolisms and phylogenetic reconstructions. * We have added a recruitment plot feature, plotting fragments against microbial genomes. * We have added the ability to view all BLAST hits for a fragment and show the individual BLAST alignments. * The ability to use [http://www.genome.ad.jp/kegg/kegg2.html KEGG] maps map explore and compare metabolic reconstructions on several hierarchy levels (e.g. the high level metabolism overview). * We have changed the pipeline that computes the underlying data so all numbers/percentages/comparisons/etc. will have changed if you look at your data in v2.0 * We have also updated the underlying databases. Most notably the [http://www.theseed.org SEED] NR no longer from represents the status from 2006, we have added the [http://www.arb-silva.de/ Silva RNA database]) * Added the <strong>Invite a friend feature</strong> to share data that you submitted with other users by just entering their email addresses. * Support for user driven creation and maintenance of groups. * The ability to support arbitrary sets and versions of databases. * Many small detailed fixes and improvements. == Databases used == * [http://www.theseed.org SEED non redundant protein database] * [http://greengenes.lbl.gov/ GREENGENES] * [http://rdp.cme.msu.edu/ RDP-II] * [http://www.arb-silva.de/ SILVA] == Standard Compliance == We are currently working with Dawn Fields and Renzo Kottmann from the GSC to support a version of "ANDREAS PLEASE SUPPLY THIS INFO" == - Page Overview == [this will be a simple graphical overview of the pages and their links] == Manual for MG-RAST v2.0 == Separate page == Tutorial (Using MG-RAST-v2.0 to analyze my metagenome sample) == Separate page == Availability== Using MG-RAST is free for all users. We provide privacy for the data submitted and MG-RAST is open source. While we currently do not provide a defined release, current snapshots of the system are available via CVS. === FAQ - Contact 828ba8db20cba15d92d6a1c96f119b514e5b523a 1821 1820 2008-06-20T17:19:43Z FolkerMeyer 2 wikitext text/x-wiki == MG-RAST v2.0 Homepage == === What is MG-RAST ( Executive Summary) === MG-RAST (Metagenome Rapid Annotation using Subsystem Technology) is a fully-automated service for annotating metagenome samples. It is the only service that we are aware of that will handle both short reads (notably reads of 109 or 230 basepairs from a [http://en.wikipedia.org/wiki/454_life_sciences#Technology 454] instrument) and longer [http://en.wikipedia.org/wiki/DNA_sequencing#Chain-termination_methods Sanger] reads or even assembled short contigs. In the MG-RAST analysis the fragments in a given sample will be compared to protein, RNA and subsystem databases. Both the submitted data and the MG-RAST analysis can be shared with other users or "published" to the public on the server, we provide stable unique identifiers for public metagenomes. === Overview === The MG-RAST system will utilize data structures and software generated in the context of [http://www.theseed.org The SEED] and [http://www.nmpdr.org NMPDR] to provide annotation of sequence fragments, their phylogenetic classification and an initial metabolic reconstruction. The service also provides means for comparing phylogenetic classifications and metabolic reconstructions of metagenomes. The service is built as a modified version of the [http://rast.nmpdr.org RAST] server, which was originally designed to support high-quality annotation of complete or draft microbial genomes. We have adapted this technology for the analysis of metagenomes. In addition to SEED data we use the following ribosomal RNA databases for our analyses: GREENGENES, RDP-II, SILVA, and European ribosomal RNA database. User submission and analysis are confidential, although each user may optionally allow a collaborative environment that enables multiple users to share datasets. In addition, users can also allow public access and request long-term storage of their metagenomic samples on the server. The server provides unique IDs for metagenomes and the sequences they contain and provides a stable mechanism for linking to. All data and analysis are available for download in a variety of different formats. To be able to contact you once the computation is finished and in case user intervention is required, we request that users register with email address. === What's new? (Changes from MG-RAST v1.2 to MG-RAST v2.0) === We have gone through several rounds of feedback with users of version 1.2 (Many thanks to all who send suggestions!) and have included the following new capabilities in version 2.0: * Significant improvements of user interface responsiveness and overall performance. * The ability to <strong>"publish" metagenomes on the MG-RAST server</strong> for public use. * The ability to <strong>download subsets</strong> of fragments as fasta (eg. all fragments matching a given eg. a [http://www.theseed.org/wiki/Glossary#Subsystem subsystem] or a [http://www.theseed.org/wiki/Glossary#Functional_role functional role]). * The ability to modify parameters for sequence comparison underlying both metabolic reconstruction and phylogenetic reconstruction on the fly. * The same capability for the heatmap style comparisons of both metabolisms and phylogenetic reconstructions. * We have added a recruitment plot feature, plotting fragments against microbial genomes. * We have added the ability to view all BLAST hits for a fragment and show the individual BLAST alignments. * The ability to use [http://www.genome.ad.jp/kegg/kegg2.html KEGG] maps map explore and compare metabolic reconstructions on several hierarchy levels (e.g. the high level metabolism overview). * We have changed the pipeline that computes the underlying data so all numbers/percentages/comparisons/etc. will have changed if you look at your data in v2.0 * We have also updated the underlying databases. Most notably the [http://www.theseed.org SEED] NR no longer from represents the status from 2006, we have added the [http://www.arb-silva.de/ Silva RNA database]) * Added the <strong>Invite a friend feature</strong> to share data that you submitted with other users by just entering their email addresses. * Support for user driven creation and maintenance of groups. * The ability to support arbitrary sets and versions of databases. * Many small detailed fixes and improvements. == Databases used == * [http://www.theseed.org SEED non redundant protein database] * [http://greengenes.lbl.gov/ GREENGENES] * [http://rdp.cme.msu.edu/ RDP-II] * [http://www.arb-silva.de/ SILVA] == Standard Compliance == We are currently working with Dawn Fields and Renzo Kottmann from the GSC to support a version of "ANDREAS PLEASE SUPPLY THIS INFO" == - Page Overview == [this will be a simple graphical overview of the pages and their links] == Manual for MG-RAST v2.0 == Separate page == Tutorial (Using MG-RAST-v2.0 to analyze my metagenome sample) == Separate page == Availability== Using MG-RAST is free for all users. We provide privacy for the data submitted and MG-RAST is open source. While we currently do not provide a defined release, current snapshots of the system are available via CVS. === Frequently asked questions (FAQ) === Separate Page === Contact === Once logged in to the system, the address of the MG-RAST system will be available to all users. e40ce938af6538396189caaff99ccec8c2f15425 1822 1821 2008-06-20T17:20:16Z FolkerMeyer 2 wikitext text/x-wiki == MG-RAST v2.0 Homepage == === What is MG-RAST ( Executive Summary) === MG-RAST (Metagenome Rapid Annotation using Subsystem Technology) is a fully-automated service for annotating metagenome samples. It is the only service that we are aware of that will handle both short reads (notably reads of 109 or 230 basepairs from a [http://en.wikipedia.org/wiki/454_life_sciences#Technology 454] instrument) and longer [http://en.wikipedia.org/wiki/DNA_sequencing#Chain-termination_methods Sanger] reads or even assembled short contigs. In the MG-RAST analysis the fragments in a given sample will be compared to protein, RNA and subsystem databases. Both the submitted data and the MG-RAST analysis can be shared with other users or "published" to the public on the server, we provide stable unique identifiers for public metagenomes. === Overview === The MG-RAST system will utilize data structures and software generated in the context of [http://www.theseed.org The SEED] and [http://www.nmpdr.org NMPDR] to provide annotation of sequence fragments, their phylogenetic classification and an initial metabolic reconstruction. The service also provides means for comparing phylogenetic classifications and metabolic reconstructions of metagenomes. The service is built as a modified version of the [http://rast.nmpdr.org RAST] server, which was originally designed to support high-quality annotation of complete or draft microbial genomes. We have adapted this technology for the analysis of metagenomes. In addition to SEED data we use the following ribosomal RNA databases for our analyses: GREENGENES, RDP-II, SILVA, and European ribosomal RNA database. User submission and analysis are confidential, although each user may optionally allow a collaborative environment that enables multiple users to share datasets. In addition, users can also allow public access and request long-term storage of their metagenomic samples on the server. The server provides unique IDs for metagenomes and the sequences they contain and provides a stable mechanism for linking to. All data and analysis are available for download in a variety of different formats. To be able to contact you once the computation is finished and in case user intervention is required, we request that users register with email address. === What's new? (Changes from MG-RAST v1.2 to MG-RAST v2.0) === We have gone through several rounds of feedback with users of version 1.2 (Many thanks to all who send suggestions!) and have included the following new capabilities in version 2.0: * Significant improvements of user interface responsiveness and overall performance. * The ability to <strong>"publish" metagenomes on the MG-RAST server</strong> for public use. * The ability to <strong>download subsets</strong> of fragments as fasta (eg. all fragments matching a given eg. a [http://www.theseed.org/wiki/Glossary#Subsystem subsystem] or a [http://www.theseed.org/wiki/Glossary#Functional_role functional role]). * The ability to modify parameters for sequence comparison underlying both metabolic reconstruction and phylogenetic reconstruction on the fly. * The same capability for the heatmap style comparisons of both metabolisms and phylogenetic reconstructions. * We have added a recruitment plot feature, plotting fragments against microbial genomes. * We have added the ability to view all BLAST hits for a fragment and show the individual BLAST alignments. * The ability to use [http://www.genome.ad.jp/kegg/kegg2.html KEGG] maps map explore and compare metabolic reconstructions on several hierarchy levels (e.g. the high level metabolism overview). * We have changed the pipeline that computes the underlying data so all numbers/percentages/comparisons/etc. will have changed if you look at your data in v2.0 * We have also updated the underlying databases. Most notably the [http://www.theseed.org SEED] NR no longer from represents the status from 2006, we have added the [http://www.arb-silva.de/ Silva RNA database]) * Added the <strong>Invite a friend feature</strong> to share data that you submitted with other users by just entering their email addresses. * Support for user driven creation and maintenance of groups. * The ability to support arbitrary sets and versions of databases. * Many small detailed fixes and improvements. == Databases used == * [http://www.theseed.org SEED non redundant protein database] * [http://greengenes.lbl.gov/ GREENGENES] * [http://rdp.cme.msu.edu/ RDP-II] * [http://www.arb-silva.de/ SILVA] == Standard Compliance == We are currently working with Dawn Fields and Renzo Kottmann from the GSC to support a version of "ANDREAS PLEASE SUPPLY THIS INFO" == Page Overview == [this will be a simple graphical overview of the pages and their links] == Manual for MG-RAST v2.0 == Separate page == Tutorial (Using MG-RAST-v2.0 to analyze my metagenome sample) == Separate page == Availability== Using MG-RAST is free for all users. We provide privacy for the data submitted and MG-RAST is open source. While we currently do not provide a defined release, current snapshots of the system are available via CVS. == Frequently asked questions (FAQ) == Separate Page == Contact == Once logged in to the system, the address of the MG-RAST system will be available to all users. 304ef6f56e03c9003fb98d6176825fba7c3150be 1823 1822 2008-06-20T17:20:53Z FolkerMeyer 2 wikitext text/x-wiki == MG-RAST v2.0 Homepage == === What is MG-RAST ( Executive Summary) === MG-RAST (Metagenome Rapid Annotation using Subsystem Technology) is a fully-automated service for annotating metagenome samples. It is the only service that we are aware of that will handle both short reads (notably reads of 109 or 230 basepairs from a [http://en.wikipedia.org/wiki/454_life_sciences#Technology 454] instrument) and longer [http://en.wikipedia.org/wiki/DNA_sequencing#Chain-termination_methods Sanger] reads or even assembled short contigs. In the MG-RAST analysis the fragments in a given sample will be compared to protein, RNA and subsystem databases. Both the submitted data and the MG-RAST analysis can be shared with other users or "published" to the public on the server, we provide stable unique identifiers for public metagenomes. === Overview === The MG-RAST system will utilize data structures and software generated in the context of [http://www.theseed.org The SEED] and [http://www.nmpdr.org NMPDR] to provide annotation of sequence fragments, their phylogenetic classification and an initial metabolic reconstruction. The service also provides means for comparing phylogenetic classifications and metabolic reconstructions of metagenomes. The service is built as a modified version of the [http://rast.nmpdr.org RAST] server, which was originally designed to support high-quality annotation of complete or draft microbial genomes. We have adapted this technology for the analysis of metagenomes. In addition to SEED data we use the following ribosomal RNA databases for our analyses: GREENGENES, RDP-II, SILVA, and European ribosomal RNA database. User submission and analysis are confidential, although each user may optionally allow a collaborative environment that enables multiple users to share datasets. In addition, users can also allow public access and request long-term storage of their metagenomic samples on the server. The server provides unique IDs for metagenomes and the sequences they contain and provides a stable mechanism for linking to. All data and analysis are available for download in a variety of different formats. To be able to contact you once the computation is finished and in case user intervention is required, we request that users register with email address. === What's new? (Changes from MG-RAST v1.2 to MG-RAST v2.0) === We have gone through several rounds of feedback with users of version 1.2 (Many thanks to all who send suggestions!) and have included the following new capabilities in version 2.0: * Significant improvements of user interface responsiveness and overall performance. * The ability to <strong>"publish" metagenomes on the MG-RAST server</strong> for public use. * The ability to <strong>download subsets</strong> of fragments as fasta (eg. all fragments matching a given eg. a [http://www.theseed.org/wiki/Glossary#Subsystem subsystem] or a [http://www.theseed.org/wiki/Glossary#Functional_role functional role]). * The ability to modify parameters for sequence comparison underlying both metabolic reconstruction and phylogenetic reconstruction on the fly. * The same capability for the heatmap style comparisons of both metabolisms and phylogenetic reconstructions. * We have added a recruitment plot feature, plotting fragments against microbial genomes. * We have added the ability to view all BLAST hits for a fragment and show the individual BLAST alignments. * The ability to use [http://www.genome.ad.jp/kegg/kegg2.html KEGG] maps map explore and compare metabolic reconstructions on several hierarchy levels (e.g. the high level metabolism overview). * We have changed the pipeline that computes the underlying data so all numbers/percentages/comparisons/etc. will have changed if you look at your data in v2.0 * We have also updated the underlying databases. Most notably the [http://www.theseed.org SEED] NR no longer from represents the status from 2006, we have added the [http://www.arb-silva.de/ Silva RNA database]) * Added the <strong>Invite a friend feature</strong> to share data that you submitted with other users by just entering their email addresses. * Support for user driven creation and maintenance of groups. * The ability to support arbitrary sets and versions of databases. * Many small detailed fixes and improvements. == Databases used == * [http://www.theseed.org SEED non redundant protein database] * [http://greengenes.lbl.gov/ GREENGENES] * [http://rdp.cme.msu.edu/ RDP-II] * [http://www.arb-silva.de/ SILVA] == Standard Compliance == We are currently working with Dawn Fields and Renzo Kottmann from the GSC to support a version of "ANDREAS PLEASE SUPPLY THIS INFO" == Navigating MG-RAST v2.0 == [this will be a simple graphical overview of the pages and their links] == Manual for MG-RAST v2.0 == Separate page == Tutorial (Using MG-RAST-v2.0 to analyze my metagenome sample) == Separate page == Availability== Using MG-RAST is free for all users. We provide privacy for the data submitted and MG-RAST is open source. While we currently do not provide a defined release, current snapshots of the system are available via CVS. == Frequently asked questions (FAQ) == Separate Page == Contact == Once logged in to the system, the address of the MG-RAST system will be available to all users. 0961f7880ed90d44240ddc33759e74be696e1a79 0 1459 1824 2008-06-20T17:37:28Z FolkerMeyer 2 wikitext text/x-wiki === What are projects? === Projects are related sets of metagenomes. If you for example plan on studying a set of samples from a chronoseries, it might me useful to group them into a project. === What level of privacy does MG-RAST v2.0 provide? === We provide password control and the ability for the submitting entity to control access on a username/password basis to the submitted data sets. === Do you support BLASTing against my private database XYZ? === We currently do not explicitly support this, however the underlying software design end system architecture support this. === How frequently do you update the underlying NR for MG-RAST? === With version 2.0 we have added the support for multiple concurrent sets of sequence similarity results to be stored per metagenome. We can add results for newer NRs. However once you start comparing results for metagenomes (say you are interested in the phylogenetic reconstruction) different versions of the NR used for the underlying data will lead to incorrect comparison results as older versions of NR will miss certain organisms and or annotations. d5778306d77124af4b041eddfe76e5fafa46736f 1830 1824 2008-06-20T17:46:27Z FolkerMeyer 2 wikitext text/x-wiki === What are projects? === Projects are related sets of metagenomes. If you for example plan on studying a set of samples from a chronoseries, it might me useful to group them into a project. === What level of privacy does MG-RAST v2.0 provide? === We provide password control and the ability for the submitting entity to control access on a username/password basis to the submitted data sets. === Do you support BLASTing against my private database XYZ? === We currently do not explicitly support this, however the underlying software design end system architecture support this. === How frequently do you update the underlying NR for MG-RAST? === With version 2.0 we have added the support for multiple concurrent sets of sequence similarity results to be stored per metagenome. We can add results for newer NRs. However once you start comparing results for metagenomes (say you are interested in the phylogenetic reconstruction) different versions of the NR used for the underlying data will lead to incorrect comparison results as older versions of NR will miss certain organisms and or annotations. === How long does it take to analyze my Metagenome? === The answer depends on two factors a) the size of your data set and b) the current server load. Under optimal conditions, it takes about 18 hours to run a 100 million basepair 454 metagenome through the pipeline. === What parameters should I use to analyze my data? === The answer depends on your sample. In any case we recommend that you modify e-value, minimal alignment length and percent identity requirements for the BLAST results underlying the results. The effects of this are different for each sample. Depending on sample complexity, sample size, number of species an diversity of species present your results will vary dramatically when modifying these parameters. For RNA based phylogenetic reconstruction, we recommend requiring a minimum alignment length of 50bp for exact matches. 90aeef851d45b1cb590155dacbf7a87290d237eb 1833 1830 2008-06-20T17:50:23Z FolkerMeyer 2 wikitext text/x-wiki === What are projects? === Projects are related sets of metagenomes. If you for example plan on studying a set of samples from a chronoseries, it might me useful to group them into a project. === What level of privacy does MG-RAST v2.0 provide? === We provide password control and the ability for the submitting entity to control access on a username/password basis to the submitted data sets. === Do you support BLASTing against my private database XYZ? === We currently do not explicitly support this, however the underlying software design end system architecture support this. === How frequently do you update the underlying NR for MG-RAST? === With version 2.0 we have added the support for multiple concurrent sets of sequence similarity results to be stored per metagenome. We can add results for newer NRs. However once you start comparing results for metagenomes (say you are interested in the phylogenetic reconstruction) different versions of the NR used for the underlying data will lead to incorrect comparison results as older versions of NR will miss certain organisms and or annotations. === How long does it take to analyze my Metagenome? === The answer depends on two factors a) the size of your data set and b) the current server load. Under optimal conditions, it takes about 18 hours to run a 100 million basepair 454 metagenome through the pipeline. === What parameters should I use to analyze my data? === The answer depends on your sample. In any case we recommend that you modify e-value, minimal alignment length and percent identity requirements for the BLAST results underlying the results. The effects of this are different for each sample. Depending on sample complexity, sample size, number of species an diversity of species present your results will vary dramatically when modifying these parameters. For RNA based phylogenetic reconstruction, we recommend requiring a minimum alignment length of 50bp for exact matches. === Where can people access the "public" metagenomes? === The MG-RAST v2.0 Homepage has a list of publicly accessible metagenomes. Future versions will continue to support this feature, also we will provide a metadata based selection tool, that will allow the user to focus on metagenome data sets from the environment or condition etc they are interested in. de7aa0d1df9e135e790553b33d3e8171590661f2 1834 1833 2008-06-20T17:50:44Z FolkerMeyer 2 /* Where can people access the "public" metagenomes? */ wikitext text/x-wiki === What are projects? === Projects are related sets of metagenomes. If you for example plan on studying a set of samples from a chronoseries, it might me useful to group them into a project. === What level of privacy does MG-RAST v2.0 provide? === We provide password control and the ability for the submitting entity to control access on a username/password basis to the submitted data sets. === Do you support BLASTing against my private database XYZ? === We currently do not explicitly support this, however the underlying software design end system architecture support this. === How frequently do you update the underlying NR for MG-RAST? === With version 2.0 we have added the support for multiple concurrent sets of sequence similarity results to be stored per metagenome. We can add results for newer NRs. However once you start comparing results for metagenomes (say you are interested in the phylogenetic reconstruction) different versions of the NR used for the underlying data will lead to incorrect comparison results as older versions of NR will miss certain organisms and or annotations. === How long does it take to analyze my Metagenome? === The answer depends on two factors a) the size of your data set and b) the current server load. Under optimal conditions, it takes about 18 hours to run a 100 million basepair 454 metagenome through the pipeline. === What parameters should I use to analyze my data? === The answer depends on your sample. In any case we recommend that you modify e-value, minimal alignment length and percent identity requirements for the BLAST results underlying the results. The effects of this are different for each sample. Depending on sample complexity, sample size, number of species an diversity of species present your results will vary dramatically when modifying these parameters. For RNA based phylogenetic reconstruction, we recommend requiring a minimum alignment length of 50bp for exact matches. === Where can people access my "published" metagenomes? === The MG-RAST v2.0 Homepage has a list of publicly accessible metagenomes. Future versions will continue to support this feature, also we will provide a metadata based selection tool, that will allow the user to focus on metagenome data sets from the environment or condition etc they are interested in. bd4a75c2f95442fc49493cf77f52c38fe1c447b6 1835 1834 2008-06-20T17:51:39Z FolkerMeyer 2 /* What level of privacy does MG-RAST v2.0 provide? */ wikitext text/x-wiki === What are projects? === Projects are related sets of metagenomes. If you for example plan on studying a set of samples from a chronoseries, it might me useful to group them into a project. === What level of privacy does MG-RAST v2.0 provide? === We provide password control and the ability for the submitting entity to control access on a username/password basis to the submitted data sets. Note that we currently do not provide industry standard encryption as this would put additional load on our server infrastructure and is not strictly required for scientific purposes. === Do you support BLASTing against my private database XYZ? === We currently do not explicitly support this, however the underlying software design end system architecture support this. === How frequently do you update the underlying NR for MG-RAST? === With version 2.0 we have added the support for multiple concurrent sets of sequence similarity results to be stored per metagenome. We can add results for newer NRs. However once you start comparing results for metagenomes (say you are interested in the phylogenetic reconstruction) different versions of the NR used for the underlying data will lead to incorrect comparison results as older versions of NR will miss certain organisms and or annotations. === How long does it take to analyze my Metagenome? === The answer depends on two factors a) the size of your data set and b) the current server load. Under optimal conditions, it takes about 18 hours to run a 100 million basepair 454 metagenome through the pipeline. === What parameters should I use to analyze my data? === The answer depends on your sample. In any case we recommend that you modify e-value, minimal alignment length and percent identity requirements for the BLAST results underlying the results. The effects of this are different for each sample. Depending on sample complexity, sample size, number of species an diversity of species present your results will vary dramatically when modifying these parameters. For RNA based phylogenetic reconstruction, we recommend requiring a minimum alignment length of 50bp for exact matches. === Where can people access my "published" metagenomes? === The MG-RAST v2.0 Homepage has a list of publicly accessible metagenomes. Future versions will continue to support this feature, also we will provide a metadata based selection tool, that will allow the user to focus on metagenome data sets from the environment or condition etc they are interested in. ac12d06ca92590373f9fd5aabb6b6c4bbbf9a38d 1836 1835 2008-06-20T17:53:02Z FolkerMeyer 2 wikitext text/x-wiki === What are projects? === Projects are related sets of metagenomes. If you for example plan on studying a set of samples from a chronoseries, it might me useful to group them into a project. === What level of privacy does MG-RAST v2.0 provide? === We provide password control and the ability for the submitting entity to control access on a username/password basis to the submitted data sets. Note that we currently do not provide industry standard encryption as this would put additional load on our server infrastructure and is not strictly required for scientific purposes. === Do you support BLASTing against my private database XYZ? === We currently do not explicitly support this, however the underlying software design end system architecture support this. === How frequently do you update the underlying NR for MG-RAST? === With version 2.0 we have added the support for multiple concurrent sets of sequence similarity results to be stored per metagenome. We can add results for newer NRs. However once you start comparing results for metagenomes (say you are interested in the phylogenetic reconstruction) different versions of the NR used for the underlying data will lead to incorrect comparison results as older versions of NR will miss certain organisms and or annotations. === How long does it take to analyze my Metagenome? === The answer depends on two factors a) the size of your data set and b) the current server load. Under optimal conditions, it takes about 18 hours to run a 100 million basepair 454 metagenome through the pipeline. === What parameters should I use to analyze my data? === The answer depends on your sample. In any case we recommend that you modify e-value, minimal alignment length and percent identity requirements for the BLAST results underlying the results. The effects of this are different for each sample. Depending on sample complexity, sample size, number of species an diversity of species present your results will vary dramatically when modifying these parameters. For RNA based phylogenetic reconstruction, we recommend requiring a minimum alignment length of 50bp for exact matches. === Where can people access my "published" metagenomes? === The MG-RAST v2.0 Homepage has a list of publicly accessible metagenomes. Future versions will continue to support this feature, also we will provide a metadata based selection tool, that will allow the user to focus on metagenome data sets from the environment or condition etc they are interested in. === What about HIPAA relevant data? === MG-RAST is provided under the assumption that all data is anonymized, no [http://en.wikipedia.org/wiki/HIPAA HIPAA] relevant data should be stored on MG-RAST. 49a5f717b5d9c12c9e55df8f0ded17900bb96f19 1837 1836 2008-06-20T17:54:15Z FolkerMeyer 2 wikitext text/x-wiki === What are projects? === Projects are related sets of metagenomes. If you for example plan on studying a set of samples from a chronoseries, it might me useful to group them into a project. === What level of privacy does MG-RAST v2.0 provide? === We provide password control and the ability for the submitting entity to control access on a username/password basis to the submitted data sets. Note that we currently do not provide industry standard encryption as this would put additional load on our server infrastructure and is not strictly required for scientific purposes. === Do you support BLASTing against my private database XYZ? === We currently do not explicitly support this, however the underlying software design end system architecture support this. === How frequently do you update the underlying NR for MG-RAST? === With version 2.0 we have added the support for multiple concurrent sets of sequence similarity results to be stored per metagenome. We can add results for newer NRs. However once you start comparing results for metagenomes (say you are interested in the phylogenetic reconstruction) different versions of the NR used for the underlying data will lead to incorrect comparison results as older versions of NR will miss certain organisms and or annotations. === How long does it take to analyze my Metagenome? === The answer depends on two factors a) the size of your data set and b) the current server load. Under optimal conditions, it takes about 18 hours to run a 100 million basepair 454 metagenome through the pipeline. === How many metagenomes can I submit? === We do not restrict user submission of samples. However the computation required is massive and samples are processed on a first come first serve basis. === What parameters should I use to analyze my data? === The answer depends on your sample. In any case we recommend that you modify e-value, minimal alignment length and percent identity requirements for the BLAST results underlying the results. The effects of this are different for each sample. Depending on sample complexity, sample size, number of species an diversity of species present your results will vary dramatically when modifying these parameters. For RNA based phylogenetic reconstruction, we recommend requiring a minimum alignment length of 50bp for exact matches. === Where can people access my "published" metagenomes? === The MG-RAST v2.0 Homepage has a list of publicly accessible metagenomes. Future versions will continue to support this feature, also we will provide a metadata based selection tool, that will allow the user to focus on metagenome data sets from the environment or condition etc they are interested in. === What about HIPAA relevant data? === MG-RAST is provided under the assumption that all data is anonymized, no [http://en.wikipedia.org/wiki/HIPAA HIPAA] relevant data should be stored on MG-RAST. f9e0cdb24a3c97f23b3d41022df9f02e15b182ef 1839 1837 2008-06-20T21:07:38Z FolkerMeyer 2 wikitext text/x-wiki === What are projects? === Projects are related sets of metagenomes. If you for example plan on studying a set of samples from a chronoseries, it might me useful to group them into a project. === What level of privacy does MG-RAST v2.0 provide? === We provide password control and the ability for the submitting entity to control access on a username/password basis to the submitted data sets. Note that we currently do not provide industry standard encryption as this would put additional load on our server infrastructure and is not strictly required for scientific purposes. === Do you support BLASTing against my private database XYZ? === We currently do not explicitly support this, however the underlying software design end system architecture support this. === How frequently do you update the underlying NR for MG-RAST? === With version 2.0 we have added the support for multiple concurrent sets of sequence similarity results to be stored per metagenome. We can add results for newer NRs. However once you start comparing results for metagenomes (say you are interested in the phylogenetic reconstruction) different versions of the NR used for the underlying data will lead to incorrect comparison results as older versions of NR will miss certain organisms and or annotations. === How long does it take to analyze my Metagenome? === The answer depends on two factors a) the size of your data set and b) the current server load. Under optimal conditions, it takes about 18 hours to run a 100 million basepair 454 metagenome through the pipeline. === How many metagenomes can I submit? === We do not restrict user submission of samples. However the computation required is massive and samples are processed on a first come first serve basis. === What parameters should I use to analyze my data? === The answer depends on your sample. In any case we recommend that you modify e-value, minimal alignment length and percent identity requirements for the BLAST results underlying the results. The effects of this are different for each sample. Depending on sample complexity, sample size, number of species an diversity of species present your results will vary dramatically when modifying these parameters. For RNA based phylogenetic reconstruction, we recommend requiring a minimum alignment length of 50bp for exact matches. === Where can people access my "published" metagenomes? === The MG-RAST v2.0 Homepage has a list of publicly accessible metagenomes. Future versions will continue to support this feature, also we will provide a metadata based selection tool, that will allow the user to focus on metagenome data sets from the environment or condition etc they are interested in. === What about HIPAA relevant data? === MG-RAST is provided under the assumption that all data is anonymized, no [http://en.wikipedia.org/wiki/HIPAA HIPAA] relevant data should be stored on MG-RAST. === How are the numbers computed? === <font color="red">NEEDS TO BE FILLED</font> b0b7fa25730b3eeb2fabc211b1c92ed998fa31f3 1844 1839 2008-06-20T22:38:59Z FolkerMeyer 2 wikitext text/x-wiki === What are projects? === Projects are related sets of metagenomes. If you for example plan on studying a set of samples from a chronoseries, it might me useful to group them into a project. === What level of privacy does MG-RAST v2.0 provide? === We provide password control and the ability for the submitting entity to control access on a username/password basis to the submitted data sets. Note that we currently do not provide industry standard encryption as this would put additional load on our server infrastructure and is not strictly required for scientific purposes. === Do you support BLASTing against my private database XYZ? === We currently do not explicitly support this, however the underlying software design end system architecture support this. === How frequently do you update the underlying NR for MG-RAST? === With version 2.0 we have added the support for multiple concurrent sets of sequence similarity results to be stored per metagenome. We can add results for newer NRs. However once you start comparing results for metagenomes (say you are interested in the phylogenetic reconstruction) different versions of the NR used for the underlying data will lead to incorrect comparison results as older versions of NR will miss certain organisms and or annotations. === How long does it take to analyze my Metagenome? === The answer depends on two factors a) the size of your data set and b) the current server load. Under optimal conditions, it takes about 18 hours to run a 100 million basepair 454 metagenome through the pipeline. === How many metagenomes can I submit? === We do not restrict user submission of samples. However the computation required is massive and samples are processed on a first come first serve basis. === What parameters should I use to analyze my data? === The answer depends on your sample. In any case we recommend that you modify e-value, minimal alignment length and percent identity requirements for the BLAST results underlying the results. The effects of this are different for each sample. Depending on sample complexity, sample size, number of species an diversity of species present your results will vary dramatically when modifying these parameters. For RNA based phylogenetic reconstruction, we recommend requiring a minimum alignment length of 50bp for exact matches. === Where can people access my "published" metagenomes? === The MG-RAST v2.0 Homepage has a list of publicly accessible metagenomes. Future versions will continue to support this feature, also we will provide a metadata based selection tool, that will allow the user to focus on metagenome data sets from the environment or condition etc they are interested in. === What about HIPAA relevant data? === MG-RAST is provided under the assumption that all data is anonymized, no [http://en.wikipedia.org/wiki/HIPAA HIPAA] relevant data should be stored on MG-RAST. === How can I download a subset of fragments in FASTA format? === Many pages support downloading the data into a spreadsheet format (eg MS Excel). One the Metabolic Reconstruction page or the Phylogenetic reconstruction, you can download a subset of the fragments contained in the sample matching a specific group of organisms or matching a specific part of metabolism via clicking on the tab for Tabular view. There you click on a given subset. === How are the numbers computed? === <font color="red">NEEDS TO BE FILLED</font> b4b18ea39d575932ce7f20cf761d893d43ed3ff1 0 1458 1825 1823 2008-06-20T17:37:52Z FolkerMeyer 2 /* Frequently asked questions (FAQ) */ wikitext text/x-wiki == MG-RAST v2.0 Homepage == === What is MG-RAST ( Executive Summary) === MG-RAST (Metagenome Rapid Annotation using Subsystem Technology) is a fully-automated service for annotating metagenome samples. It is the only service that we are aware of that will handle both short reads (notably reads of 109 or 230 basepairs from a [http://en.wikipedia.org/wiki/454_life_sciences#Technology 454] instrument) and longer [http://en.wikipedia.org/wiki/DNA_sequencing#Chain-termination_methods Sanger] reads or even assembled short contigs. In the MG-RAST analysis the fragments in a given sample will be compared to protein, RNA and subsystem databases. Both the submitted data and the MG-RAST analysis can be shared with other users or "published" to the public on the server, we provide stable unique identifiers for public metagenomes. === Overview === The MG-RAST system will utilize data structures and software generated in the context of [http://www.theseed.org The SEED] and [http://www.nmpdr.org NMPDR] to provide annotation of sequence fragments, their phylogenetic classification and an initial metabolic reconstruction. The service also provides means for comparing phylogenetic classifications and metabolic reconstructions of metagenomes. The service is built as a modified version of the [http://rast.nmpdr.org RAST] server, which was originally designed to support high-quality annotation of complete or draft microbial genomes. We have adapted this technology for the analysis of metagenomes. In addition to SEED data we use the following ribosomal RNA databases for our analyses: GREENGENES, RDP-II, SILVA, and European ribosomal RNA database. User submission and analysis are confidential, although each user may optionally allow a collaborative environment that enables multiple users to share datasets. In addition, users can also allow public access and request long-term storage of their metagenomic samples on the server. The server provides unique IDs for metagenomes and the sequences they contain and provides a stable mechanism for linking to. All data and analysis are available for download in a variety of different formats. To be able to contact you once the computation is finished and in case user intervention is required, we request that users register with email address. === What's new? (Changes from MG-RAST v1.2 to MG-RAST v2.0) === We have gone through several rounds of feedback with users of version 1.2 (Many thanks to all who send suggestions!) and have included the following new capabilities in version 2.0: * Significant improvements of user interface responsiveness and overall performance. * The ability to <strong>"publish" metagenomes on the MG-RAST server</strong> for public use. * The ability to <strong>download subsets</strong> of fragments as fasta (eg. all fragments matching a given eg. a [http://www.theseed.org/wiki/Glossary#Subsystem subsystem] or a [http://www.theseed.org/wiki/Glossary#Functional_role functional role]). * The ability to modify parameters for sequence comparison underlying both metabolic reconstruction and phylogenetic reconstruction on the fly. * The same capability for the heatmap style comparisons of both metabolisms and phylogenetic reconstructions. * We have added a recruitment plot feature, plotting fragments against microbial genomes. * We have added the ability to view all BLAST hits for a fragment and show the individual BLAST alignments. * The ability to use [http://www.genome.ad.jp/kegg/kegg2.html KEGG] maps map explore and compare metabolic reconstructions on several hierarchy levels (e.g. the high level metabolism overview). * We have changed the pipeline that computes the underlying data so all numbers/percentages/comparisons/etc. will have changed if you look at your data in v2.0 * We have also updated the underlying databases. Most notably the [http://www.theseed.org SEED] NR no longer from represents the status from 2006, we have added the [http://www.arb-silva.de/ Silva RNA database]) * Added the <strong>Invite a friend feature</strong> to share data that you submitted with other users by just entering their email addresses. * Support for user driven creation and maintenance of groups. * The ability to support arbitrary sets and versions of databases. * Many small detailed fixes and improvements. == Databases used == * [http://www.theseed.org SEED non redundant protein database] * [http://greengenes.lbl.gov/ GREENGENES] * [http://rdp.cme.msu.edu/ RDP-II] * [http://www.arb-silva.de/ SILVA] == Standard Compliance == We are currently working with Dawn Fields and Renzo Kottmann from the GSC to support a version of "ANDREAS PLEASE SUPPLY THIS INFO" == Navigating MG-RAST v2.0 == [this will be a simple graphical overview of the pages and their links] == Manual for MG-RAST v2.0 == Separate page == Tutorial (Using MG-RAST-v2.0 to analyze my metagenome sample) == Separate page == Availability== Using MG-RAST is free for all users. We provide privacy for the data submitted and MG-RAST is open source. While we currently do not provide a defined release, current snapshots of the system are available via CVS. == [[MG_RAST_v2.0_FAQ Frequently asked questions (FAQ)]] == == Contact == Once logged in to the system, the address of the MG-RAST system will be available to all users. 949d9dc0ea22696b6abde334318a579d399fa4d2 1826 1825 2008-06-20T17:38:41Z FolkerMeyer 2 wikitext text/x-wiki == MG-RAST v2.0 Homepage == === What is MG-RAST ( Executive Summary) === MG-RAST (Metagenome Rapid Annotation using Subsystem Technology) is a fully-automated service for annotating metagenome samples. It is the only service that we are aware of that will handle both short reads (notably reads of 109 or 230 basepairs from a [http://en.wikipedia.org/wiki/454_life_sciences#Technology 454] instrument) and longer [http://en.wikipedia.org/wiki/DNA_sequencing#Chain-termination_methods Sanger] reads or even assembled short contigs. In the MG-RAST analysis the fragments in a given sample will be compared to protein, RNA and subsystem databases. Both the submitted data and the MG-RAST analysis can be shared with other users or "published" to the public on the server, we provide stable unique identifiers for public metagenomes. === Overview === The MG-RAST system will utilize data structures and software generated in the context of [http://www.theseed.org The SEED] and [http://www.nmpdr.org NMPDR] to provide annotation of sequence fragments, their phylogenetic classification and an initial metabolic reconstruction. The service also provides means for comparing phylogenetic classifications and metabolic reconstructions of metagenomes. The service is built as a modified version of the [http://rast.nmpdr.org RAST] server, which was originally designed to support high-quality annotation of complete or draft microbial genomes. We have adapted this technology for the analysis of metagenomes. In addition to SEED data we use the following ribosomal RNA databases for our analyses: GREENGENES, RDP-II, SILVA, and European ribosomal RNA database. User submission and analysis are confidential, although each user may optionally allow a collaborative environment that enables multiple users to share datasets. In addition, users can also allow public access and request long-term storage of their metagenomic samples on the server. The server provides unique IDs for metagenomes and the sequences they contain and provides a stable mechanism for linking to. All data and analysis are available for download in a variety of different formats. To be able to contact you once the computation is finished and in case user intervention is required, we request that users register with email address. === What's new? (Changes from MG-RAST v1.2 to MG-RAST v2.0) === We have gone through several rounds of feedback with users of version 1.2 (Many thanks to all who send suggestions!) and have included the following new capabilities in version 2.0: * Significant improvements of user interface responsiveness and overall performance. * The ability to <strong>"publish" metagenomes on the MG-RAST server</strong> for public use. * The ability to <strong>download subsets</strong> of fragments as fasta (eg. all fragments matching a given eg. a [http://www.theseed.org/wiki/Glossary#Subsystem subsystem] or a [http://www.theseed.org/wiki/Glossary#Functional_role functional role]). * The ability to modify parameters for sequence comparison underlying both metabolic reconstruction and phylogenetic reconstruction on the fly. * The same capability for the heatmap style comparisons of both metabolisms and phylogenetic reconstructions. * We have added a recruitment plot feature, plotting fragments against microbial genomes. * We have added the ability to view all BLAST hits for a fragment and show the individual BLAST alignments. * The ability to use [http://www.genome.ad.jp/kegg/kegg2.html KEGG] maps map explore and compare metabolic reconstructions on several hierarchy levels (e.g. the high level metabolism overview). * We have changed the pipeline that computes the underlying data so all numbers/percentages/comparisons/etc. will have changed if you look at your data in v2.0 * We have also updated the underlying databases. Most notably the [http://www.theseed.org SEED] NR no longer from represents the status from 2006, we have added the [http://www.arb-silva.de/ Silva RNA database]) * Added the <strong>Invite a friend feature</strong> to share data that you submitted with other users by just entering their email addresses. * Support for user driven creation and maintenance of groups. * The ability to support arbitrary sets and versions of databases. * Many small detailed fixes and improvements. == Databases used == * [http://www.theseed.org SEED non redundant protein database] * [http://greengenes.lbl.gov/ GREENGENES] * [http://rdp.cme.msu.edu/ RDP-II] * [http://www.arb-silva.de/ SILVA] == Standard Compliance == We are currently working with Dawn Fields and Renzo Kottmann from the GSC to support a version of "ANDREAS PLEASE SUPPLY THIS INFO" == Navigating MG-RAST v2.0 == [this will be a simple graphical overview of the pages and their links] == Manual for MG-RAST v2.0 == Separate page == Tutorial (Using MG-RAST-v2.0 to analyze my metagenome sample) == Separate page == Availability== Using MG-RAST is free for all users. We provide privacy for the data submitted and MG-RAST is open source. While we currently do not provide a defined release, current snapshots of the system are available via CVS. == [[MG_RAST_v2.0_FAQ| Frequently asked questions (FAQ)]] == == Contact == Once logged in to the system, the address of the MG-RAST system will be available to all users. 53941cf9a937bc00d3290f7d72954a96a47ac449 1827 1826 2008-06-20T17:40:04Z FolkerMeyer 2 wikitext text/x-wiki == MG-RAST v2.0 Homepage == === What is MG-RAST ( Executive Summary) === MG-RAST (Metagenome Rapid Annotation using Subsystem Technology) is a fully-automated service for annotating metagenome samples. It is the only service that we are aware of that will handle both short reads (notably reads of 109 or 230 basepairs from a [http://en.wikipedia.org/wiki/454_life_sciences#Technology 454] instrument) and longer [http://en.wikipedia.org/wiki/DNA_sequencing#Chain-termination_methods Sanger] reads or even assembled short contigs. In the MG-RAST analysis the fragments in a given sample will be compared to protein, RNA and subsystem databases. Both the submitted data and the MG-RAST analysis can be shared with other users or "published" to the public on the server, we provide stable unique identifiers for public metagenomes. === Overview === The MG-RAST system will utilize data structures and software generated in the context of [http://www.theseed.org The SEED] and [http://www.nmpdr.org NMPDR] to provide annotation of sequence fragments, their phylogenetic classification and an initial metabolic reconstruction. The service also provides means for comparing phylogenetic classifications and metabolic reconstructions of metagenomes. The service is built as a modified version of the [http://rast.nmpdr.org RAST] server, which was originally designed to support high-quality annotation of complete or draft microbial genomes. We have adapted this technology for the analysis of metagenomes. In addition to SEED data we use the following ribosomal RNA databases for our analyses: GREENGENES, RDP-II, SILVA, and European ribosomal RNA database. User submission and analysis are confidential, although each user may optionally allow a collaborative environment that enables multiple users to share datasets. In addition, users can also allow public access and request long-term storage of their metagenomic samples on the server. The server provides unique IDs for metagenomes and the sequences they contain and provides a stable mechanism for linking to. All data and analysis are available for download in a variety of different formats. To be able to contact you once the computation is finished and in case user intervention is required, we request that users register with email address. === What's new? (Changes from MG-RAST v1.2 to MG-RAST v2.0) === We have gone through several rounds of feedback with users of version 1.2 (Many thanks to all who send suggestions!) and have included the following new capabilities in version 2.0: * Significant improvements of user interface responsiveness and overall performance. * The ability to <strong>"publish" metagenomes on the MG-RAST server</strong> for public use. * The ability to <strong>download subsets</strong> of fragments as fasta (eg. all fragments matching a given eg. a [http://www.theseed.org/wiki/Glossary#Subsystem subsystem] or a [http://www.theseed.org/wiki/Glossary#Functional_role functional role]). * The ability to modify parameters for sequence comparison underlying both metabolic reconstruction and phylogenetic reconstruction on the fly. * The same capability for the heatmap style comparisons of both metabolisms and phylogenetic reconstructions. * We have added a recruitment plot feature, plotting fragments against microbial genomes. * We have added the ability to view all BLAST hits for a fragment and show the individual BLAST alignments. * The ability to use [http://www.genome.ad.jp/kegg/kegg2.html KEGG] maps map explore and compare metabolic reconstructions on several hierarchy levels (e.g. the high level metabolism overview). * We have changed the pipeline that computes the underlying data so all numbers/percentages/comparisons/etc. will have changed if you look at your data in v2.0 * We have also updated the underlying databases. Most notably the [http://www.theseed.org SEED] NR no longer from represents the status from 2006, we have added the [http://www.arb-silva.de/ Silva RNA database]) * Added the <strong>Invite a friend feature</strong> to share data that you submitted with other users by just entering their email addresses. * Support for user driven creation and maintenance of groups. * The ability to support arbitrary sets and versions of databases. * Many small detailed fixes and improvements. == Databases used == * [http://www.theseed.org SEED non redundant protein database] * [http://greengenes.lbl.gov/ GREENGENES] * [http://rdp.cme.msu.edu/ RDP-II] * [http://www.arb-silva.de/ SILVA] == Standard Compliance == We are currently working with Dawn Fields and Renzo Kottmann from the GSC to support a version of "ANDREAS PLEASE SUPPLY THIS INFO" == Navigating MG-RAST v2.0 == [this will be a simple graphical overview of the pages and their links] == Manual for MG-RAST v2.0 == Separate page == Tutorial (Using MG-RAST-v2.0 to analyze my metagenome sample) == Separate page == Availability== Using MG-RAST is free for all users. We provide privacy for the data submitted and MG-RAST is open source. While we currently do not provide a defined release, current snapshots of the system are available via CVS. == [[MG_RAST_v2.0_FAQ]] == #| Frequently asked questions (FAQ)]] == == Contact == Once logged in to the system, the address of the MG-RAST system will be available to all users. 7612e6b54c611df20e536f9b36b36b35e471a8db 1828 1827 2008-06-20T17:40:40Z FolkerMeyer 2 wikitext text/x-wiki == MG-RAST v2.0 Homepage == === What is MG-RAST ( Executive Summary) === MG-RAST (Metagenome Rapid Annotation using Subsystem Technology) is a fully-automated service for annotating metagenome samples. It is the only service that we are aware of that will handle both short reads (notably reads of 109 or 230 basepairs from a [http://en.wikipedia.org/wiki/454_life_sciences#Technology 454] instrument) and longer [http://en.wikipedia.org/wiki/DNA_sequencing#Chain-termination_methods Sanger] reads or even assembled short contigs. In the MG-RAST analysis the fragments in a given sample will be compared to protein, RNA and subsystem databases. Both the submitted data and the MG-RAST analysis can be shared with other users or "published" to the public on the server, we provide stable unique identifiers for public metagenomes. === Overview === The MG-RAST system will utilize data structures and software generated in the context of [http://www.theseed.org The SEED] and [http://www.nmpdr.org NMPDR] to provide annotation of sequence fragments, their phylogenetic classification and an initial metabolic reconstruction. The service also provides means for comparing phylogenetic classifications and metabolic reconstructions of metagenomes. The service is built as a modified version of the [http://rast.nmpdr.org RAST] server, which was originally designed to support high-quality annotation of complete or draft microbial genomes. We have adapted this technology for the analysis of metagenomes. In addition to SEED data we use the following ribosomal RNA databases for our analyses: GREENGENES, RDP-II, SILVA, and European ribosomal RNA database. User submission and analysis are confidential, although each user may optionally allow a collaborative environment that enables multiple users to share datasets. In addition, users can also allow public access and request long-term storage of their metagenomic samples on the server. The server provides unique IDs for metagenomes and the sequences they contain and provides a stable mechanism for linking to. All data and analysis are available for download in a variety of different formats. To be able to contact you once the computation is finished and in case user intervention is required, we request that users register with email address. === What's new? (Changes from MG-RAST v1.2 to MG-RAST v2.0) === We have gone through several rounds of feedback with users of version 1.2 (Many thanks to all who send suggestions!) and have included the following new capabilities in version 2.0: * Significant improvements of user interface responsiveness and overall performance. * The ability to <strong>"publish" metagenomes on the MG-RAST server</strong> for public use. * The ability to <strong>download subsets</strong> of fragments as fasta (eg. all fragments matching a given eg. a [http://www.theseed.org/wiki/Glossary#Subsystem subsystem] or a [http://www.theseed.org/wiki/Glossary#Functional_role functional role]). * The ability to modify parameters for sequence comparison underlying both metabolic reconstruction and phylogenetic reconstruction on the fly. * The same capability for the heatmap style comparisons of both metabolisms and phylogenetic reconstructions. * We have added a recruitment plot feature, plotting fragments against microbial genomes. * We have added the ability to view all BLAST hits for a fragment and show the individual BLAST alignments. * The ability to use [http://www.genome.ad.jp/kegg/kegg2.html KEGG] maps map explore and compare metabolic reconstructions on several hierarchy levels (e.g. the high level metabolism overview). * We have changed the pipeline that computes the underlying data so all numbers/percentages/comparisons/etc. will have changed if you look at your data in v2.0 * We have also updated the underlying databases. Most notably the [http://www.theseed.org SEED] NR no longer from represents the status from 2006, we have added the [http://www.arb-silva.de/ Silva RNA database]) * Added the <strong>Invite a friend feature</strong> to share data that you submitted with other users by just entering their email addresses. * Support for user driven creation and maintenance of groups. * The ability to support arbitrary sets and versions of databases. * Many small detailed fixes and improvements. == Databases used == * [http://www.theseed.org SEED non redundant protein database] * [http://greengenes.lbl.gov/ GREENGENES] * [http://rdp.cme.msu.edu/ RDP-II] * [http://www.arb-silva.de/ SILVA] == Standard Compliance == We are currently working with Dawn Fields and Renzo Kottmann from the GSC to support a version of "ANDREAS PLEASE SUPPLY THIS INFO" == Navigating MG-RAST v2.0 == [this will be a simple graphical overview of the pages and their links] == Manual for MG-RAST v2.0 == Separate page == Tutorial (Using MG-RAST-v2.0 to analyze my metagenome sample) == Separate page == Availability== Using MG-RAST is free for all users. We provide privacy for the data submitted and MG-RAST is open source. While we currently do not provide a defined release, current snapshots of the system are available via CVS. == Frequently asked questions (FAQ)]] == We provide a list of frequently asked questions at [[MG_RAST_v2.0_FAQ]]. == Contact == Once logged in to the system, the address of the MG-RAST system will be available to all users. 649db28a0c68bd147cbfb741420393ff62a88939 1829 1828 2008-06-20T17:40:51Z FolkerMeyer 2 /* Frequently asked questions (FAQ)]] */ wikitext text/x-wiki == MG-RAST v2.0 Homepage == === What is MG-RAST ( Executive Summary) === MG-RAST (Metagenome Rapid Annotation using Subsystem Technology) is a fully-automated service for annotating metagenome samples. It is the only service that we are aware of that will handle both short reads (notably reads of 109 or 230 basepairs from a [http://en.wikipedia.org/wiki/454_life_sciences#Technology 454] instrument) and longer [http://en.wikipedia.org/wiki/DNA_sequencing#Chain-termination_methods Sanger] reads or even assembled short contigs. In the MG-RAST analysis the fragments in a given sample will be compared to protein, RNA and subsystem databases. Both the submitted data and the MG-RAST analysis can be shared with other users or "published" to the public on the server, we provide stable unique identifiers for public metagenomes. === Overview === The MG-RAST system will utilize data structures and software generated in the context of [http://www.theseed.org The SEED] and [http://www.nmpdr.org NMPDR] to provide annotation of sequence fragments, their phylogenetic classification and an initial metabolic reconstruction. The service also provides means for comparing phylogenetic classifications and metabolic reconstructions of metagenomes. The service is built as a modified version of the [http://rast.nmpdr.org RAST] server, which was originally designed to support high-quality annotation of complete or draft microbial genomes. We have adapted this technology for the analysis of metagenomes. In addition to SEED data we use the following ribosomal RNA databases for our analyses: GREENGENES, RDP-II, SILVA, and European ribosomal RNA database. User submission and analysis are confidential, although each user may optionally allow a collaborative environment that enables multiple users to share datasets. In addition, users can also allow public access and request long-term storage of their metagenomic samples on the server. The server provides unique IDs for metagenomes and the sequences they contain and provides a stable mechanism for linking to. All data and analysis are available for download in a variety of different formats. To be able to contact you once the computation is finished and in case user intervention is required, we request that users register with email address. === What's new? (Changes from MG-RAST v1.2 to MG-RAST v2.0) === We have gone through several rounds of feedback with users of version 1.2 (Many thanks to all who send suggestions!) and have included the following new capabilities in version 2.0: * Significant improvements of user interface responsiveness and overall performance. * The ability to <strong>"publish" metagenomes on the MG-RAST server</strong> for public use. * The ability to <strong>download subsets</strong> of fragments as fasta (eg. all fragments matching a given eg. a [http://www.theseed.org/wiki/Glossary#Subsystem subsystem] or a [http://www.theseed.org/wiki/Glossary#Functional_role functional role]). * The ability to modify parameters for sequence comparison underlying both metabolic reconstruction and phylogenetic reconstruction on the fly. * The same capability for the heatmap style comparisons of both metabolisms and phylogenetic reconstructions. * We have added a recruitment plot feature, plotting fragments against microbial genomes. * We have added the ability to view all BLAST hits for a fragment and show the individual BLAST alignments. * The ability to use [http://www.genome.ad.jp/kegg/kegg2.html KEGG] maps map explore and compare metabolic reconstructions on several hierarchy levels (e.g. the high level metabolism overview). * We have changed the pipeline that computes the underlying data so all numbers/percentages/comparisons/etc. will have changed if you look at your data in v2.0 * We have also updated the underlying databases. Most notably the [http://www.theseed.org SEED] NR no longer from represents the status from 2006, we have added the [http://www.arb-silva.de/ Silva RNA database]) * Added the <strong>Invite a friend feature</strong> to share data that you submitted with other users by just entering their email addresses. * Support for user driven creation and maintenance of groups. * The ability to support arbitrary sets and versions of databases. * Many small detailed fixes and improvements. == Databases used == * [http://www.theseed.org SEED non redundant protein database] * [http://greengenes.lbl.gov/ GREENGENES] * [http://rdp.cme.msu.edu/ RDP-II] * [http://www.arb-silva.de/ SILVA] == Standard Compliance == We are currently working with Dawn Fields and Renzo Kottmann from the GSC to support a version of "ANDREAS PLEASE SUPPLY THIS INFO" == Navigating MG-RAST v2.0 == [this will be a simple graphical overview of the pages and their links] == Manual for MG-RAST v2.0 == Separate page == Tutorial (Using MG-RAST-v2.0 to analyze my metagenome sample) == Separate page == Availability== Using MG-RAST is free for all users. We provide privacy for the data submitted and MG-RAST is open source. While we currently do not provide a defined release, current snapshots of the system are available via CVS. == Frequently asked questions (FAQ) == We provide a list of frequently asked questions at [[MG_RAST_v2.0_FAQ]]. == Contact == Once logged in to the system, the address of the MG-RAST system will be available to all users. efd7944e62948b998e140d237ef9e25942b007e0 1831 1829 2008-06-20T17:48:13Z FolkerMeyer 2 /* What's new? (Changes from MG-RAST v1.2 to MG-RAST v2.0) */ wikitext text/x-wiki == MG-RAST v2.0 Homepage == === What is MG-RAST ( Executive Summary) === MG-RAST (Metagenome Rapid Annotation using Subsystem Technology) is a fully-automated service for annotating metagenome samples. It is the only service that we are aware of that will handle both short reads (notably reads of 109 or 230 basepairs from a [http://en.wikipedia.org/wiki/454_life_sciences#Technology 454] instrument) and longer [http://en.wikipedia.org/wiki/DNA_sequencing#Chain-termination_methods Sanger] reads or even assembled short contigs. In the MG-RAST analysis the fragments in a given sample will be compared to protein, RNA and subsystem databases. Both the submitted data and the MG-RAST analysis can be shared with other users or "published" to the public on the server, we provide stable unique identifiers for public metagenomes. === Overview === The MG-RAST system will utilize data structures and software generated in the context of [http://www.theseed.org The SEED] and [http://www.nmpdr.org NMPDR] to provide annotation of sequence fragments, their phylogenetic classification and an initial metabolic reconstruction. The service also provides means for comparing phylogenetic classifications and metabolic reconstructions of metagenomes. The service is built as a modified version of the [http://rast.nmpdr.org RAST] server, which was originally designed to support high-quality annotation of complete or draft microbial genomes. We have adapted this technology for the analysis of metagenomes. In addition to SEED data we use the following ribosomal RNA databases for our analyses: GREENGENES, RDP-II, SILVA, and European ribosomal RNA database. User submission and analysis are confidential, although each user may optionally allow a collaborative environment that enables multiple users to share datasets. In addition, users can also allow public access and request long-term storage of their metagenomic samples on the server. The server provides unique IDs for metagenomes and the sequences they contain and provides a stable mechanism for linking to. All data and analysis are available for download in a variety of different formats. To be able to contact you once the computation is finished and in case user intervention is required, we request that users register with email address. === What's new? (Changes from MG-RAST v1.2 to MG-RAST v2.0) === We have gone through several rounds of feedback with users of version 1.2 (Many thanks to all who send suggestions!) and have included the following new capabilities in version 2.0: * Significant improvements of user interface responsiveness and overall performance. * The ability to <strong>"publish" metagenomes on the MG-RAST server</strong> for public use. * The ability to <strong>download subsets</strong> of fragments as fasta (eg. all fragments matching a given eg. a [http://www.theseed.org/wiki/Glossary#Subsystem subsystem] or a [http://www.theseed.org/wiki/Glossary#Functional_role functional role]). * The <strong>ability to modify parameters for sequence comparison</strong> underlying both metabolic reconstruction and phylogenetic reconstruction on the fly. * The same capability for the heatmap style comparisons of both metabolisms and phylogenetic reconstructions. * We have added a <strong> recruitment plot </strong>feature, plotting fragments against microbial genomes. * We have added the ability to <strong> view all BLAST hits for a fragment </strong> and show the individual BLAST alignments. * The ability to use [http://www.genome.ad.jp/kegg/kegg2.html KEGG] maps map explore and compare metabolic reconstructions on several hierarchy levels (e.g. the high level metabolism overview). * We have changed the pipeline that computes the underlying data so all numbers/percentages/comparisons/etc. will have changed if you look at your data in v2.0 * We have also updated the underlying databases. Most notably the [http://www.theseed.org SEED] NR no longer from represents the status from 2006, we have added the [http://www.arb-silva.de/ Silva RNA database]) * Added the <strong>Invite a friend feature</strong> to share data that you submitted with other users by just entering their email addresses. * Support for user driven creation and maintenance of groups. * The ability to support arbitrary sets and versions of databases. * Many small detailed fixes and improvements. == Databases used == * [http://www.theseed.org SEED non redundant protein database] * [http://greengenes.lbl.gov/ GREENGENES] * [http://rdp.cme.msu.edu/ RDP-II] * [http://www.arb-silva.de/ SILVA] == Standard Compliance == We are currently working with Dawn Fields and Renzo Kottmann from the GSC to support a version of "ANDREAS PLEASE SUPPLY THIS INFO" == Navigating MG-RAST v2.0 == [this will be a simple graphical overview of the pages and their links] == Manual for MG-RAST v2.0 == Separate page == Tutorial (Using MG-RAST-v2.0 to analyze my metagenome sample) == Separate page == Availability== Using MG-RAST is free for all users. We provide privacy for the data submitted and MG-RAST is open source. While we currently do not provide a defined release, current snapshots of the system are available via CVS. == Frequently asked questions (FAQ) == We provide a list of frequently asked questions at [[MG_RAST_v2.0_FAQ]]. == Contact == Once logged in to the system, the address of the MG-RAST system will be available to all users. 51b279c69626e38d25860ed00941f7952cd58bfe 1832 1831 2008-06-20T17:48:30Z FolkerMeyer 2 /* What's new? (Changes from MG-RAST v1.2 to MG-RAST v2.0) */ wikitext text/x-wiki == MG-RAST v2.0 Homepage == === What is MG-RAST ( Executive Summary) === MG-RAST (Metagenome Rapid Annotation using Subsystem Technology) is a fully-automated service for annotating metagenome samples. It is the only service that we are aware of that will handle both short reads (notably reads of 109 or 230 basepairs from a [http://en.wikipedia.org/wiki/454_life_sciences#Technology 454] instrument) and longer [http://en.wikipedia.org/wiki/DNA_sequencing#Chain-termination_methods Sanger] reads or even assembled short contigs. In the MG-RAST analysis the fragments in a given sample will be compared to protein, RNA and subsystem databases. Both the submitted data and the MG-RAST analysis can be shared with other users or "published" to the public on the server, we provide stable unique identifiers for public metagenomes. === Overview === The MG-RAST system will utilize data structures and software generated in the context of [http://www.theseed.org The SEED] and [http://www.nmpdr.org NMPDR] to provide annotation of sequence fragments, their phylogenetic classification and an initial metabolic reconstruction. The service also provides means for comparing phylogenetic classifications and metabolic reconstructions of metagenomes. The service is built as a modified version of the [http://rast.nmpdr.org RAST] server, which was originally designed to support high-quality annotation of complete or draft microbial genomes. We have adapted this technology for the analysis of metagenomes. In addition to SEED data we use the following ribosomal RNA databases for our analyses: GREENGENES, RDP-II, SILVA, and European ribosomal RNA database. User submission and analysis are confidential, although each user may optionally allow a collaborative environment that enables multiple users to share datasets. In addition, users can also allow public access and request long-term storage of their metagenomic samples on the server. The server provides unique IDs for metagenomes and the sequences they contain and provides a stable mechanism for linking to. All data and analysis are available for download in a variety of different formats. To be able to contact you once the computation is finished and in case user intervention is required, we request that users register with email address. === What's new? (Changes from MG-RAST v1.2 to MG-RAST v2.0) === We have gone through several rounds of feedback with users of version 1.2 (Many thanks to all who send suggestions!) and have included the following new capabilities in version 2.0: * Significant improvements of user interface responsiveness and overall performance. * The ability to <strong>"publish" metagenomes on the MG-RAST server</strong> for public use. * The ability to <strong>download subsets</strong> of fragments as fasta (eg. all fragments matching a given eg. a [http://www.theseed.org/wiki/Glossary#Subsystem subsystem] or a [http://www.theseed.org/wiki/Glossary#Functional_role functional role]). * The <strong>ability to modify parameters for sequence comparison</strong> underlying both metabolic reconstruction and phylogenetic reconstruction on the fly. * The same capability for the heatmap style comparisons of both metabolisms and phylogenetic reconstructions. * We have added a <strong> recruitment plot </strong>feature, plotting fragments against microbial genomes. * We have added the ability to <strong> view all BLAST hits for a fragment </strong> and show the individual BLAST alignments. * The ability to use [http://www.genome.ad.jp/kegg/kegg2.html KEGG] maps map explore and compare metabolic reconstructions on several hierarchy levels (e.g. the high level metabolism overview). * We have changed the pipeline that computes the underlying data so all numbers/percentages/comparisons/etc. will have changed if you look at your data in v2.0 * We have also <strong>updated the underlying databases</strong>. Most notably the [http://www.theseed.org SEED] NR no longer from represents the status from 2006, we have added the [http://www.arb-silva.de/ Silva RNA database]) * Added the <strong>Invite a friend feature</strong> to share data that you submitted with other users by just entering their email addresses. * Support for user driven creation and maintenance of groups. * The ability to support arbitrary sets and versions of databases. * Many small detailed fixes and improvements. == Databases used == * [http://www.theseed.org SEED non redundant protein database] * [http://greengenes.lbl.gov/ GREENGENES] * [http://rdp.cme.msu.edu/ RDP-II] * [http://www.arb-silva.de/ SILVA] == Standard Compliance == We are currently working with Dawn Fields and Renzo Kottmann from the GSC to support a version of "ANDREAS PLEASE SUPPLY THIS INFO" == Navigating MG-RAST v2.0 == [this will be a simple graphical overview of the pages and their links] == Manual for MG-RAST v2.0 == Separate page == Tutorial (Using MG-RAST-v2.0 to analyze my metagenome sample) == Separate page == Availability== Using MG-RAST is free for all users. We provide privacy for the data submitted and MG-RAST is open source. While we currently do not provide a defined release, current snapshots of the system are available via CVS. == Frequently asked questions (FAQ) == We provide a list of frequently asked questions at [[MG_RAST_v2.0_FAQ]]. == Contact == Once logged in to the system, the address of the MG-RAST system will be available to all users. 008eeb0d6573fca6087c5e8b70f4580258df7747 1838 1832 2008-06-20T18:11:21Z FolkerMeyer 2 /* What's new? (Changes from MG-RAST v1.2 to MG-RAST v2.0) */ wikitext text/x-wiki == MG-RAST v2.0 Homepage == === What is MG-RAST ( Executive Summary) === MG-RAST (Metagenome Rapid Annotation using Subsystem Technology) is a fully-automated service for annotating metagenome samples. It is the only service that we are aware of that will handle both short reads (notably reads of 109 or 230 basepairs from a [http://en.wikipedia.org/wiki/454_life_sciences#Technology 454] instrument) and longer [http://en.wikipedia.org/wiki/DNA_sequencing#Chain-termination_methods Sanger] reads or even assembled short contigs. In the MG-RAST analysis the fragments in a given sample will be compared to protein, RNA and subsystem databases. Both the submitted data and the MG-RAST analysis can be shared with other users or "published" to the public on the server, we provide stable unique identifiers for public metagenomes. === Overview === The MG-RAST system will utilize data structures and software generated in the context of [http://www.theseed.org The SEED] and [http://www.nmpdr.org NMPDR] to provide annotation of sequence fragments, their phylogenetic classification and an initial metabolic reconstruction. The service also provides means for comparing phylogenetic classifications and metabolic reconstructions of metagenomes. The service is built as a modified version of the [http://rast.nmpdr.org RAST] server, which was originally designed to support high-quality annotation of complete or draft microbial genomes. We have adapted this technology for the analysis of metagenomes. In addition to SEED data we use the following ribosomal RNA databases for our analyses: GREENGENES, RDP-II, SILVA, and European ribosomal RNA database. User submission and analysis are confidential, although each user may optionally allow a collaborative environment that enables multiple users to share datasets. In addition, users can also allow public access and request long-term storage of their metagenomic samples on the server. The server provides unique IDs for metagenomes and the sequences they contain and provides a stable mechanism for linking to. All data and analysis are available for download in a variety of different formats. To be able to contact you once the computation is finished and in case user intervention is required, we request that users register with email address. === What's new in v2.0? (Changes from MG-RAST v1.2) === We have gone through several rounds of feedback with users of version 1.2 (Many thanks to all who send suggestions!) and have included the following new capabilities in version 2.0: * Significant improvements of user interface responsiveness and overall performance. * The ability to <strong>"publish" metagenomes on the MG-RAST server</strong> for public use. * The ability to <strong>download subsets</strong> of fragments as fasta (eg. all fragments matching a given eg. a [http://www.theseed.org/wiki/Glossary#Subsystem subsystem] or a [http://www.theseed.org/wiki/Glossary#Functional_role functional role]). * The <strong>ability to modify parameters for sequence comparison</strong> underlying both metabolic reconstruction and phylogenetic reconstruction on the fly. * The same capability for the heatmap style comparisons of both metabolisms and phylogenetic reconstructions. * We have added a <strong> recruitment plot </strong>feature, plotting fragments against microbial genomes. * We have added the ability to <strong> view all BLAST hits for a fragment </strong> and show the individual BLAST alignments. * The ability to use [http://www.genome.ad.jp/kegg/kegg2.html KEGG] maps map explore and compare metabolic reconstructions on several hierarchy levels (e.g. the high level metabolism overview). * We have changed the pipeline that computes the underlying data so all numbers/percentages/comparisons/etc. will have changed if you look at your data in v2.0 * We have also <strong>updated the underlying databases</strong>. Most notably the [http://www.theseed.org SEED] NR no longer from represents the status from 2006, we have added the [http://www.arb-silva.de/ Silva RNA database]) * Added the <strong>Invite a friend feature</strong> to share data that you submitted with other users by just entering their email addresses. * Support for user driven creation and maintenance of groups. * The ability to support arbitrary sets and versions of databases. * Many small detailed fixes and improvements. == Databases used == * [http://www.theseed.org SEED non redundant protein database] * [http://greengenes.lbl.gov/ GREENGENES] * [http://rdp.cme.msu.edu/ RDP-II] * [http://www.arb-silva.de/ SILVA] == Standard Compliance == We are currently working with Dawn Fields and Renzo Kottmann from the GSC to support a version of "ANDREAS PLEASE SUPPLY THIS INFO" == Navigating MG-RAST v2.0 == [this will be a simple graphical overview of the pages and their links] == Manual for MG-RAST v2.0 == Separate page == Tutorial (Using MG-RAST-v2.0 to analyze my metagenome sample) == Separate page == Availability== Using MG-RAST is free for all users. We provide privacy for the data submitted and MG-RAST is open source. While we currently do not provide a defined release, current snapshots of the system are available via CVS. == Frequently asked questions (FAQ) == We provide a list of frequently asked questions at [[MG_RAST_v2.0_FAQ]]. == Contact == Once logged in to the system, the address of the MG-RAST system will be available to all users. 53dae6ad3b1e87213c299275300cfb0d04753217 1842 1838 2008-06-20T22:30:09Z FolkerMeyer 2 /* Navigating MG-RAST v2.0 */ wikitext text/x-wiki == MG-RAST v2.0 Homepage == === What is MG-RAST ( Executive Summary) === MG-RAST (Metagenome Rapid Annotation using Subsystem Technology) is a fully-automated service for annotating metagenome samples. It is the only service that we are aware of that will handle both short reads (notably reads of 109 or 230 basepairs from a [http://en.wikipedia.org/wiki/454_life_sciences#Technology 454] instrument) and longer [http://en.wikipedia.org/wiki/DNA_sequencing#Chain-termination_methods Sanger] reads or even assembled short contigs. In the MG-RAST analysis the fragments in a given sample will be compared to protein, RNA and subsystem databases. Both the submitted data and the MG-RAST analysis can be shared with other users or "published" to the public on the server, we provide stable unique identifiers for public metagenomes. === Overview === The MG-RAST system will utilize data structures and software generated in the context of [http://www.theseed.org The SEED] and [http://www.nmpdr.org NMPDR] to provide annotation of sequence fragments, their phylogenetic classification and an initial metabolic reconstruction. The service also provides means for comparing phylogenetic classifications and metabolic reconstructions of metagenomes. The service is built as a modified version of the [http://rast.nmpdr.org RAST] server, which was originally designed to support high-quality annotation of complete or draft microbial genomes. We have adapted this technology for the analysis of metagenomes. In addition to SEED data we use the following ribosomal RNA databases for our analyses: GREENGENES, RDP-II, SILVA, and European ribosomal RNA database. User submission and analysis are confidential, although each user may optionally allow a collaborative environment that enables multiple users to share datasets. In addition, users can also allow public access and request long-term storage of their metagenomic samples on the server. The server provides unique IDs for metagenomes and the sequences they contain and provides a stable mechanism for linking to. All data and analysis are available for download in a variety of different formats. To be able to contact you once the computation is finished and in case user intervention is required, we request that users register with email address. === What's new in v2.0? (Changes from MG-RAST v1.2) === We have gone through several rounds of feedback with users of version 1.2 (Many thanks to all who send suggestions!) and have included the following new capabilities in version 2.0: * Significant improvements of user interface responsiveness and overall performance. * The ability to <strong>"publish" metagenomes on the MG-RAST server</strong> for public use. * The ability to <strong>download subsets</strong> of fragments as fasta (eg. all fragments matching a given eg. a [http://www.theseed.org/wiki/Glossary#Subsystem subsystem] or a [http://www.theseed.org/wiki/Glossary#Functional_role functional role]). * The <strong>ability to modify parameters for sequence comparison</strong> underlying both metabolic reconstruction and phylogenetic reconstruction on the fly. * The same capability for the heatmap style comparisons of both metabolisms and phylogenetic reconstructions. * We have added a <strong> recruitment plot </strong>feature, plotting fragments against microbial genomes. * We have added the ability to <strong> view all BLAST hits for a fragment </strong> and show the individual BLAST alignments. * The ability to use [http://www.genome.ad.jp/kegg/kegg2.html KEGG] maps map explore and compare metabolic reconstructions on several hierarchy levels (e.g. the high level metabolism overview). * We have changed the pipeline that computes the underlying data so all numbers/percentages/comparisons/etc. will have changed if you look at your data in v2.0 * We have also <strong>updated the underlying databases</strong>. Most notably the [http://www.theseed.org SEED] NR no longer from represents the status from 2006, we have added the [http://www.arb-silva.de/ Silva RNA database]) * Added the <strong>Invite a friend feature</strong> to share data that you submitted with other users by just entering their email addresses. * Support for user driven creation and maintenance of groups. * The ability to support arbitrary sets and versions of databases. * Many small detailed fixes and improvements. == Databases used == * [http://www.theseed.org SEED non redundant protein database] * [http://greengenes.lbl.gov/ GREENGENES] * [http://rdp.cme.msu.edu/ RDP-II] * [http://www.arb-silva.de/ SILVA] == Standard Compliance == We are currently working with Dawn Fields and Renzo Kottmann from the GSC to support a version of "ANDREAS PLEASE SUPPLY THIS INFO" == Navigating MG-RAST v2.0 == [this will be a simple graphical overview of the pages and their links] [Image:MG-Rast Navigation Overview.jpg] == Manual for MG-RAST v2.0 == Separate page == Tutorial (Using MG-RAST-v2.0 to analyze my metagenome sample) == Separate page == Availability== Using MG-RAST is free for all users. We provide privacy for the data submitted and MG-RAST is open source. While we currently do not provide a defined release, current snapshots of the system are available via CVS. == Frequently asked questions (FAQ) == We provide a list of frequently asked questions at [[MG_RAST_v2.0_FAQ]]. == Contact == Once logged in to the system, the address of the MG-RAST system will be available to all users. 6ebdac5dba6f1e6b8df7d9d4bf35d66a4b47770b 1843 1842 2008-06-20T22:30:51Z FolkerMeyer 2 /* Navigating MG-RAST v2.0 */ wikitext text/x-wiki == MG-RAST v2.0 Homepage == === What is MG-RAST ( Executive Summary) === MG-RAST (Metagenome Rapid Annotation using Subsystem Technology) is a fully-automated service for annotating metagenome samples. It is the only service that we are aware of that will handle both short reads (notably reads of 109 or 230 basepairs from a [http://en.wikipedia.org/wiki/454_life_sciences#Technology 454] instrument) and longer [http://en.wikipedia.org/wiki/DNA_sequencing#Chain-termination_methods Sanger] reads or even assembled short contigs. In the MG-RAST analysis the fragments in a given sample will be compared to protein, RNA and subsystem databases. Both the submitted data and the MG-RAST analysis can be shared with other users or "published" to the public on the server, we provide stable unique identifiers for public metagenomes. === Overview === The MG-RAST system will utilize data structures and software generated in the context of [http://www.theseed.org The SEED] and [http://www.nmpdr.org NMPDR] to provide annotation of sequence fragments, their phylogenetic classification and an initial metabolic reconstruction. The service also provides means for comparing phylogenetic classifications and metabolic reconstructions of metagenomes. The service is built as a modified version of the [http://rast.nmpdr.org RAST] server, which was originally designed to support high-quality annotation of complete or draft microbial genomes. We have adapted this technology for the analysis of metagenomes. In addition to SEED data we use the following ribosomal RNA databases for our analyses: GREENGENES, RDP-II, SILVA, and European ribosomal RNA database. User submission and analysis are confidential, although each user may optionally allow a collaborative environment that enables multiple users to share datasets. In addition, users can also allow public access and request long-term storage of their metagenomic samples on the server. The server provides unique IDs for metagenomes and the sequences they contain and provides a stable mechanism for linking to. All data and analysis are available for download in a variety of different formats. To be able to contact you once the computation is finished and in case user intervention is required, we request that users register with email address. === What's new in v2.0? (Changes from MG-RAST v1.2) === We have gone through several rounds of feedback with users of version 1.2 (Many thanks to all who send suggestions!) and have included the following new capabilities in version 2.0: * Significant improvements of user interface responsiveness and overall performance. * The ability to <strong>"publish" metagenomes on the MG-RAST server</strong> for public use. * The ability to <strong>download subsets</strong> of fragments as fasta (eg. all fragments matching a given eg. a [http://www.theseed.org/wiki/Glossary#Subsystem subsystem] or a [http://www.theseed.org/wiki/Glossary#Functional_role functional role]). * The <strong>ability to modify parameters for sequence comparison</strong> underlying both metabolic reconstruction and phylogenetic reconstruction on the fly. * The same capability for the heatmap style comparisons of both metabolisms and phylogenetic reconstructions. * We have added a <strong> recruitment plot </strong>feature, plotting fragments against microbial genomes. * We have added the ability to <strong> view all BLAST hits for a fragment </strong> and show the individual BLAST alignments. * The ability to use [http://www.genome.ad.jp/kegg/kegg2.html KEGG] maps map explore and compare metabolic reconstructions on several hierarchy levels (e.g. the high level metabolism overview). * We have changed the pipeline that computes the underlying data so all numbers/percentages/comparisons/etc. will have changed if you look at your data in v2.0 * We have also <strong>updated the underlying databases</strong>. Most notably the [http://www.theseed.org SEED] NR no longer from represents the status from 2006, we have added the [http://www.arb-silva.de/ Silva RNA database]) * Added the <strong>Invite a friend feature</strong> to share data that you submitted with other users by just entering their email addresses. * Support for user driven creation and maintenance of groups. * The ability to support arbitrary sets and versions of databases. * Many small detailed fixes and improvements. == Databases used == * [http://www.theseed.org SEED non redundant protein database] * [http://greengenes.lbl.gov/ GREENGENES] * [http://rdp.cme.msu.edu/ RDP-II] * [http://www.arb-silva.de/ SILVA] == Standard Compliance == We are currently working with Dawn Fields and Renzo Kottmann from the GSC to support a version of "ANDREAS PLEASE SUPPLY THIS INFO" == Navigating MG-RAST v2.0 == [[Image:MG-Rast Navigation Overview.jpg]] == Manual for MG-RAST v2.0 == Separate page == Tutorial (Using MG-RAST-v2.0 to analyze my metagenome sample) == Separate page == Availability== Using MG-RAST is free for all users. We provide privacy for the data submitted and MG-RAST is open source. While we currently do not provide a defined release, current snapshots of the system are available via CVS. == Frequently asked questions (FAQ) == We provide a list of frequently asked questions at [[MG_RAST_v2.0_FAQ]]. == Contact == Once logged in to the system, the address of the MG-RAST system will be available to all users. 212db7ae77493c3671613fada5e5d1ac0a026679 1846 1843 2008-06-28T22:24:16Z FolkerMeyer 2 /* Tutorial (Using MG-RAST-v2.0 to analyze my metagenome sample) */ wikitext text/x-wiki == MG-RAST v2.0 Homepage == === What is MG-RAST ( Executive Summary) === MG-RAST (Metagenome Rapid Annotation using Subsystem Technology) is a fully-automated service for annotating metagenome samples. It is the only service that we are aware of that will handle both short reads (notably reads of 109 or 230 basepairs from a [http://en.wikipedia.org/wiki/454_life_sciences#Technology 454] instrument) and longer [http://en.wikipedia.org/wiki/DNA_sequencing#Chain-termination_methods Sanger] reads or even assembled short contigs. In the MG-RAST analysis the fragments in a given sample will be compared to protein, RNA and subsystem databases. Both the submitted data and the MG-RAST analysis can be shared with other users or "published" to the public on the server, we provide stable unique identifiers for public metagenomes. === Overview === The MG-RAST system will utilize data structures and software generated in the context of [http://www.theseed.org The SEED] and [http://www.nmpdr.org NMPDR] to provide annotation of sequence fragments, their phylogenetic classification and an initial metabolic reconstruction. The service also provides means for comparing phylogenetic classifications and metabolic reconstructions of metagenomes. The service is built as a modified version of the [http://rast.nmpdr.org RAST] server, which was originally designed to support high-quality annotation of complete or draft microbial genomes. We have adapted this technology for the analysis of metagenomes. In addition to SEED data we use the following ribosomal RNA databases for our analyses: GREENGENES, RDP-II, SILVA, and European ribosomal RNA database. User submission and analysis are confidential, although each user may optionally allow a collaborative environment that enables multiple users to share datasets. In addition, users can also allow public access and request long-term storage of their metagenomic samples on the server. The server provides unique IDs for metagenomes and the sequences they contain and provides a stable mechanism for linking to. All data and analysis are available for download in a variety of different formats. To be able to contact you once the computation is finished and in case user intervention is required, we request that users register with email address. === What's new in v2.0? (Changes from MG-RAST v1.2) === We have gone through several rounds of feedback with users of version 1.2 (Many thanks to all who send suggestions!) and have included the following new capabilities in version 2.0: * Significant improvements of user interface responsiveness and overall performance. * The ability to <strong>"publish" metagenomes on the MG-RAST server</strong> for public use. * The ability to <strong>download subsets</strong> of fragments as fasta (eg. all fragments matching a given eg. a [http://www.theseed.org/wiki/Glossary#Subsystem subsystem] or a [http://www.theseed.org/wiki/Glossary#Functional_role functional role]). * The <strong>ability to modify parameters for sequence comparison</strong> underlying both metabolic reconstruction and phylogenetic reconstruction on the fly. * The same capability for the heatmap style comparisons of both metabolisms and phylogenetic reconstructions. * We have added a <strong> recruitment plot </strong>feature, plotting fragments against microbial genomes. * We have added the ability to <strong> view all BLAST hits for a fragment </strong> and show the individual BLAST alignments. * The ability to use [http://www.genome.ad.jp/kegg/kegg2.html KEGG] maps map explore and compare metabolic reconstructions on several hierarchy levels (e.g. the high level metabolism overview). * We have changed the pipeline that computes the underlying data so all numbers/percentages/comparisons/etc. will have changed if you look at your data in v2.0 * We have also <strong>updated the underlying databases</strong>. Most notably the [http://www.theseed.org SEED] NR no longer from represents the status from 2006, we have added the [http://www.arb-silva.de/ Silva RNA database]) * Added the <strong>Invite a friend feature</strong> to share data that you submitted with other users by just entering their email addresses. * Support for user driven creation and maintenance of groups. * The ability to support arbitrary sets and versions of databases. * Many small detailed fixes and improvements. == Databases used == * [http://www.theseed.org SEED non redundant protein database] * [http://greengenes.lbl.gov/ GREENGENES] * [http://rdp.cme.msu.edu/ RDP-II] * [http://www.arb-silva.de/ SILVA] == Standard Compliance == We are currently working with Dawn Fields and Renzo Kottmann from the GSC to support a version of "ANDREAS PLEASE SUPPLY THIS INFO" == Navigating MG-RAST v2.0 == [[Image:MG-Rast Navigation Overview.jpg]] == Manual for MG-RAST v2.0 == Separate page == Tutorial (Using MG-RAST-v2.0 to analyze my metagenome sample) == A [[MG_RAST_v2.0_tutorial|tour]] of the user interface. == Availability== Using MG-RAST is free for all users. We provide privacy for the data submitted and MG-RAST is open source. While we currently do not provide a defined release, current snapshots of the system are available via CVS. == Frequently asked questions (FAQ) == We provide a list of frequently asked questions at [[MG_RAST_v2.0_FAQ]]. == Contact == Once logged in to the system, the address of the MG-RAST system will be available to all users. 1ec66406d2272ebbf2f657cca4b4b6813ddfb1b5 6 1460 1840 2008-06-20T22:28:11Z FolkerMeyer 2 wikitext text/x-wiki da39a3ee5e6b4b0d3255bfef95601890afd80709 6 1461 1841 2008-06-20T22:29:41Z FolkerMeyer 2 wikitext text/x-wiki da39a3ee5e6b4b0d3255bfef95601890afd80709 0 1462 1845 2008-06-27T23:45:13Z FolkerMeyer 2 wikitext text/x-wiki This page will contain a tutorial for version 2.0 of MG-RAST. db457fd0de5be7fda865bb9edbafd297297cbc4e 1849 1845 2008-09-08T22:03:11Z Marland 16 wikitext text/x-wiki == '''MG-RAST Tutorial''' == Start Page The start page of MG-RAST provides users with access to registration, data submission and management tools for uploaded data. Access to public genomes is also available once you login. Only once you have logged in and have selected a metagenome, can you gain access to your jobs, view your results and use comparative tools. '''Registration''' Registering for the first time? → Choose '''New Account'''. Please enter your first and last name as well as your email address into the registration form. Then please select your country and choose a login name. It's recommended to use only letters and digits for your login name, without spaces. You will then shortly receive an email with more information about the registration. Already have an account for one of our other services? → Choose Existing Account. Please enter your login and email of that account. If your group administrator has given you a group name, please enter it in the group name field, otherwise leave this field blank. '''Upload a Genome/Creating a Job''' Uploading your metagenome has a few steps. The first is uploading your fasta file. File requirements and suggestions: • The fasta file name must end in .fa, .fasta, .fas, .fsa, or .fna. • Files larger than 30 MB should compress (.tgz) their file or contact us for other options. • Quality files (.qual) may also be included along with the sequence file for submission to MG-RAST. The quality file should be combines into a single archive (that ends in .tgz) and then uploaded to the server. How to I create a .tgz file? Example: create the file metagenome.tar.gz from two fna files. tar -cvzf metagenome.tar.gz seqfile1.fna seqfile2.fna The second step requires that you provide a project name, a name for your metagenome and a brief description of the sample. The second tab shows an Upload Summary of the number of files uploaded for submission. The third and last step asks for users to supply information about the metagenome sample. These description fields were adopted from MIGs (Minimum Information about a Genome Sequence) specification. You can also elect to make your metagenome publicly available, this option is also available if you wish to do so at a later date. During this step you also have the option of removing duplicate sequences from the analysis. '''Jobs Overview''' The overall status of your metagenome analyses can be viewed from the main portion of the Jobs Overview page. This contains information regarding a user’s personal jobs and all that are public. Information includes each job/metagenome and its status and contains information including job number, name of the user who started the job, metagenome name, and annotation progress. The table of jobs can be sorted on Job ID or searchable (text boxes in header row). This is especially useful when the user has numerous metagenomes to select from. Clicking on the bars for a given job in the annotation progress column directs the user to the “Job Details” page where the detailed job status and access to the metagenome analysis can be found. ''' Job Details''' Here you are able to: • Share with selected users by providing their email addresses. • Make the metagenome publicly accessible • View detailed information on the processing of your job. • View your results!! • Download your results!! '''Overview''' The overview page has several sections, the first being the overall statistics of your sample. How these numbers were calculated can be found here (http://www.theseed.org/wiki/MG-RAST_Numbers). The second section is a summary table of taxonomic distribution based on best protein similarity to SEED and 16S based similarity to RDP. The third section is the statistical summary in paragraph form along with graphical representations of sequence length and GC distributions. The last section outlines the metagenome description and MIGS data you submitted along with your sequence file. The navigation bar has new options not previously seen on the start page or job management pages. Now you have access to tools that will allow you to compare your metagenome to other metagenomes in regard to metabolism and phylogeny (Fragment Profile). Also available is metabolic comparisons against bacterial genomes (also known as a recruitment plot). ''' Fragment Profile''' To view your metabolic or phylogenetic profiles, first select the category. Once a category is selected you can then choose your dataset in which to based you profile. For metabolic reconstructions the Subsystem dataset is available. For phylogeny, RDP, Silva, European Ribosomal and GREENGENES are all options. Parameters are also changeable; users can change e-value, p-value, percent identity, and minimum alignment length. This will allow you to refine the analysis to suit the sequence characteristics of your sample. We recommend a minimal alignment length of 50bp be used with all RNA databases. * Note: Metabolic reconstructions are based on SEED functional roles and Subsystems. (There is also a tool to view this via KEGG maps and do comparisons by going to the “Compare Metagenomes” link in the navigation bar.) Profile results are presented in two ways: Pie chart and table. Phylogeny and Metabolism are hierarchical and the pie charts reflect that notion. By clicking on a section of the pie chart, an additional chart appears detailing the breakdown of that group. This is possible down to a third level. All selections made to the chart are reflected in the accompanying table (second tab). The numbers shown in the chart and table are actual counts. '''Compare Metagenome to other Metagenomes - Heat Maps''' You can compare the metabolism or phylogeny of your metagenome with one more other metagenomes. Just as was seen looking at the Fragment Profile, you can select your database and modify your parameters. For metabolic reconstructions the Subsystem dataset is available. For phylogeny, RDP, Silva, European Ribosomal and GREENGENES are all options. Parameters are also changeable; users can change e-value, p-value, percent identity, and minimum alignment length. This will allow you to refine the analysis to suit the sequence characteristics of your sample. We recommend a minimal alignment length of 50bp be used with all RNA databases. The Heat Maps show the relative abundance, which is calculated using the number of sequences in a subsystem/tax class as a fraction of the total number of sequences in a subsystem/dataset. This allows for correction based on the sample size. '''Compare Metagenome to Organism - Recruitment Plot''' You can compare metabolism of your sample with the metabolic reconstructions from bacterial genomes. Choosing an organism predicted in your sample, you can compare the metabolic coverage. Like most of the comparative tools in MG-RAST you can modify the parameters of the calculated Metabolic Reconstruction including e-value, p-value , percent identity and minimum alignment length. '''Compare Metagenome – KEGG Map ''' MG-RAST also enables users to view their sample on KEGG maps and compare with others. Mapping of functional roles to KEGG maps was done using functional assignments from analysis against the SEED. Absolute counts are provided for each KEGG map. These maps are hierarchical, just like the Subsystems, which allow you to browse the sample on various levels or compare it with other metagenomes. 734e6b6cd519ed29fa770222f9ea8d2e3987804d 0 1433 1847 1799 2008-07-10T15:52:01Z MarkDsouza 23 wikitext text/x-wiki ===Overview=== The metagenomics RAST server (http://metagenomics.nmpdr.org) is a SEED-based environment that allows users to upload metagenomes for automated analyses. The server is built as a modified version of the RAST server. The RAST (Rapid Annotation using Subsystem Technology) technology was originally implemented to allow automated high-quality annotation of complete or draft microbial genomes using SEED data, and has been adapted for metagenome analysis.. Our freely available server provides the annotation of sequence fragments, their phylogenetic classification, functional classification of samples, and comparison between multiple metagenomes. The server also computes an initial metabolic reconstruction for the metagenome and allows comparison of metabolic reconstructions of metagenomes and genomes. User submission and analysis are confidential. Although we do not guarantee a maximum turnover time, the current average processing time is about 24 hours. Currently the server handles 454 and Sanger sequence data. Data sets supplied by 454 can be uploaded directly. In either case, the data needs to be in [[Valid fasta format]]. For more information, please see [[Which Sequences Should I Upload, and Where]]. For the metagenomics service please also read this explanation of [[metagenomics sequence formats]]. The server relies on the technology and data established by FIG and the NMPDR team at Argonne National Laboratory and the University of Chicago. In addition to SEED data we use the following ribosomal RNA databases for our analyses: [http://greengenes.lbl.gov/cgi-bin/nph-index.cgi greengenes], [http://rdp.cme.msu.edu/ RDP-II] and [http://bioinformatics.psb.ugent.be/webtools/rRNA/ European ribosomal RNA database]. ===Registration=== Registration is required for metagenome submission and viewing of results. This enables us to contact users once the computation is finished and in case the users intervention is required. At the bottom of the main page is a like for registration (see Figure 1). [[Image:mg-rast-main-page.jpeg]] Required fields for registration include first and last name and your valid email address. Login information and other communication regarding the status of your metagenome analysis job(s) will be sent to the email address you provide. Optional information includes your organization and any notes you would like to send the rast server support team. Please note that your login and password are valid for use in both the MG-RAST and RAST servers. ===Submitting a Job=== Once you have registered and logged into the server, you will be directed to your Jobs Overview. At the top of this page will be a link labeled "Upload Genome" which will allow you to start a new job. Your metagenome file(s) should be uploaded as either a single plain text file containing all the sequences in FASTA format, or a gzip compressed tar archive (tar.gz) that has your FASTA sequences. Please do not upload uncompressed files larger than 30 MB. If your data set is larger, use the compressed format or contact us for other options. If you would like, you can also include the quality files in your archive. The fasta file names should end either *.fna, *.fa, or *.fasta, and the quality files should be named *.qual. The quality files are not currently used in the analysis, but the sequences will be renamed and renumbered along with the fasta sequences. If you have trouble with the upload format please email mg-rast@mcs.anl.gov and we'll be happy to help. ''Data entered into the server will not be used for any purposes or integrated into the main SEED environment, it will remain on this server for 120 days or until deleted by the submitting user.'' An email will be sent once the automatic annotation has finished or in case user intervention is required. ===Viewing Results=== The overall status of your metagenome analyses can be viewed from the main portion of the Jobs Overview page. This contains information regarding a user’s personal jobs and when applicable, jobs of the user’s organization. Information includes each job/metagenome and its status and contains information including job number, name of the user who started the job, metagenome name, and annotation progress. The table of jobs can be sorted on any column containing textual information. When the user has numerous metagenomes to select from, they can use the text boxes in the table header to search and refine the list of jobs. Clicking on the bars for a given job in the annotation progress column directs the user to the “Job Details” page where the detailed job status and access to the metagenome analysis can be found ("Browse annotated genome in SEED Viewer"). Users can also download the results in compressed GenBank format. ===MetaGenome Overview=== The MetaGenome Overview provides the user with various statistics regarding their metagenome and details on how each of these numbers are calculated can be found [[MG-RAST_Numbers|here]]. [[Image:MG-RAST-sample-overview.png]] Users can search for a given function, subsystem or process in the table, or browse the Subsystem Overview. At the top right hand side of the page is a set of tabs that offer a wide set of information to browse, explore, compare and download. Browse allows users to look through the features of this metagenome either graphically or through a table. Both allow quick navigation and filtering for features of your interest. Each feature is linked to its own detail page. Explore allows users to view scenarios. Scenarios are isolated metabolic divisions that in aggregate represent the metabolic functionality of the metagenome. Each scenario is tested for reaction availability against the annotated functions. They provide the foundation for generating a metabolic reconstruction. Comparison of two metagenomes is also possible via the compare tab. You can also export all information about this metagenome (e.g. annotations, scenarios, subsystems) into a variety of formats (e.g. EMBL, Excel) for further analysis on your own system. ==16S Sequences== The metagenomics-RAST is primarily designed to handle random community genomes. At the moment, we only provide rudimentary support for 16S DNA sequence analysis, although this is near the very top of our to-do list. Our colleagues at San Diego State University have developed two different tools for handling 16S rDNA sequences. FastGroup, a stand-alone java application ([http://www.ncbi.nlm.nih.gov/pubmed/11707150?ordinalpos=2&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Seguritan V and Rohwer F. (2001) FastGroup: a program to dereplicate libraries of 16S rDNA sequences]. BMC Bioinformatics. 2:9. Epub 2001 Oct 16.) is the original program, and it was updated to FastGroupII ([http://www.ncbi.nlm.nih.gov/pubmed/16464253?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Yu Y, Breitbart M, McNairnie P, and Rohwer F. (2006) FastGroupII: a web-based bioinformatics platform for analyses of large 16S rDNA libraries]. BMC Bioinformatics. Feb 7;7:57.). We have provided some [[instructions for using FastGroupII with large data sets]]. We recommend FastGroupII for clustering and primary analysis of 16S libraries, and then the data from that can be fed into RDP Classifier and other programs. e6492d24c563519d9c4854a19913073a7e5d9943 1848 1847 2008-07-10T15:52:37Z MarkDsouza 23 wikitext text/x-wiki ===Overview=== The metagenomics RAST server (http://metagenomics.nmpdr.org) is a SEED-based environment that allows users to upload metagenomes for automated analyses. The server is built as a modified version of the RAST server. The RAST (Rapid Annotation using Subsystem Technology) technology was originally implemented to allow automated high-quality annotation of complete or draft microbial genomes using SEED data, and has been adapted for metagenome analysis. Our freely available server provides the annotation of sequence fragments, their phylogenetic classification, functional classification of samples, and comparison between multiple metagenomes. The server also computes an initial metabolic reconstruction for the metagenome and allows comparison of metabolic reconstructions of metagenomes and genomes. User submission and analysis are confidential. Although we do not guarantee a maximum turnover time, the current average processing time is about 24 hours. Currently the server handles 454 and Sanger sequence data. Data sets supplied by 454 can be uploaded directly. In either case, the data needs to be in [[Valid fasta format]]. For more information, please see [[Which Sequences Should I Upload, and Where]]. For the metagenomics service please also read this explanation of [[metagenomics sequence formats]]. The server relies on the technology and data established by FIG and the NMPDR team at Argonne National Laboratory and the University of Chicago. In addition to SEED data we use the following ribosomal RNA databases for our analyses: [http://greengenes.lbl.gov/cgi-bin/nph-index.cgi greengenes], [http://rdp.cme.msu.edu/ RDP-II] and [http://bioinformatics.psb.ugent.be/webtools/rRNA/ European ribosomal RNA database]. ===Registration=== Registration is required for metagenome submission and viewing of results. This enables us to contact users once the computation is finished and in case the users intervention is required. At the bottom of the main page is a like for registration (see Figure 1). [[Image:mg-rast-main-page.jpeg]] Required fields for registration include first and last name and your valid email address. Login information and other communication regarding the status of your metagenome analysis job(s) will be sent to the email address you provide. Optional information includes your organization and any notes you would like to send the rast server support team. Please note that your login and password are valid for use in both the MG-RAST and RAST servers. ===Submitting a Job=== Once you have registered and logged into the server, you will be directed to your Jobs Overview. At the top of this page will be a link labeled "Upload Genome" which will allow you to start a new job. Your metagenome file(s) should be uploaded as either a single plain text file containing all the sequences in FASTA format, or a gzip compressed tar archive (tar.gz) that has your FASTA sequences. Please do not upload uncompressed files larger than 30 MB. If your data set is larger, use the compressed format or contact us for other options. If you would like, you can also include the quality files in your archive. The fasta file names should end either *.fna, *.fa, or *.fasta, and the quality files should be named *.qual. The quality files are not currently used in the analysis, but the sequences will be renamed and renumbered along with the fasta sequences. If you have trouble with the upload format please email mg-rast@mcs.anl.gov and we'll be happy to help. ''Data entered into the server will not be used for any purposes or integrated into the main SEED environment, it will remain on this server for 120 days or until deleted by the submitting user.'' An email will be sent once the automatic annotation has finished or in case user intervention is required. ===Viewing Results=== The overall status of your metagenome analyses can be viewed from the main portion of the Jobs Overview page. This contains information regarding a user’s personal jobs and when applicable, jobs of the user’s organization. Information includes each job/metagenome and its status and contains information including job number, name of the user who started the job, metagenome name, and annotation progress. The table of jobs can be sorted on any column containing textual information. When the user has numerous metagenomes to select from, they can use the text boxes in the table header to search and refine the list of jobs. Clicking on the bars for a given job in the annotation progress column directs the user to the “Job Details” page where the detailed job status and access to the metagenome analysis can be found ("Browse annotated genome in SEED Viewer"). Users can also download the results in compressed GenBank format. ===MetaGenome Overview=== The MetaGenome Overview provides the user with various statistics regarding their metagenome and details on how each of these numbers are calculated can be found [[MG-RAST_Numbers|here]]. [[Image:MG-RAST-sample-overview.png]] Users can search for a given function, subsystem or process in the table, or browse the Subsystem Overview. At the top right hand side of the page is a set of tabs that offer a wide set of information to browse, explore, compare and download. Browse allows users to look through the features of this metagenome either graphically or through a table. Both allow quick navigation and filtering for features of your interest. Each feature is linked to its own detail page. Explore allows users to view scenarios. Scenarios are isolated metabolic divisions that in aggregate represent the metabolic functionality of the metagenome. Each scenario is tested for reaction availability against the annotated functions. They provide the foundation for generating a metabolic reconstruction. Comparison of two metagenomes is also possible via the compare tab. You can also export all information about this metagenome (e.g. annotations, scenarios, subsystems) into a variety of formats (e.g. EMBL, Excel) for further analysis on your own system. ==16S Sequences== The metagenomics-RAST is primarily designed to handle random community genomes. At the moment, we only provide rudimentary support for 16S DNA sequence analysis, although this is near the very top of our to-do list. Our colleagues at San Diego State University have developed two different tools for handling 16S rDNA sequences. FastGroup, a stand-alone java application ([http://www.ncbi.nlm.nih.gov/pubmed/11707150?ordinalpos=2&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Seguritan V and Rohwer F. (2001) FastGroup: a program to dereplicate libraries of 16S rDNA sequences]. BMC Bioinformatics. 2:9. Epub 2001 Oct 16.) is the original program, and it was updated to FastGroupII ([http://www.ncbi.nlm.nih.gov/pubmed/16464253?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Yu Y, Breitbart M, McNairnie P, and Rohwer F. (2006) FastGroupII: a web-based bioinformatics platform for analyses of large 16S rDNA libraries]. BMC Bioinformatics. Feb 7;7:57.). We have provided some [[instructions for using FastGroupII with large data sets]]. We recommend FastGroupII for clustering and primary analysis of 16S libraries, and then the data from that can be fed into RDP Classifier and other programs. 0c2bb44fd50ca89317ee98d37193ebd7bf5c0d4f 0 1463 1850 2008-10-31T13:38:49Z TobiasPaczian 17 wikitext text/x-wiki The SEED is a framework to support comparative analysis and annotation of genomes. The SEED Viewer allows you to explore the curated genomes that have been produced by a cooperative effort that includes Fellowship for Interpretation of Genomes (FIG), Argonne National Laboratory, the University of Chicago and teams from a number of other institutions. These pages will cover the usage of the different pages within the Seed Viewer. === Home === === Subsystem Select === === Subsystems === === Functional Role === === FigFams === === Annotation === === Evidence === === Blast === === Sequence === === Browse Genome === === Organism Select === === Organism Overview === === Kegg === 822577a28f2ca9bee920930917fe64b7c2dcff3f 1852 1850 2008-11-18T10:38:30Z DanielaBartels 10 /* Home */ wikitext text/x-wiki The SEED is a framework to support comparative analysis and annotation of genomes. The SEED Viewer allows you to explore the curated genomes that have been produced by a cooperative effort that includes Fellowship for Interpretation of Genomes (FIG), Argonne National Laboratory, the University of Chicago and teams from a number of other institutions. These pages will cover the usage of the different pages within the Seed Viewer. === Home === [[Image:Home.png]] === Subsystem Select === === Subsystems === === Functional Role === === FigFams === === Annotation === === Evidence === === Blast === === Sequence === === Browse Genome === === Organism Select === === Organism Overview === === Kegg === c9471b43417f7cb32ff9a21572b03bb164100ed0 1853 1852 2008-11-18T10:47:37Z DanielaBartels 10 /* Home */ wikitext text/x-wiki The SEED is a framework to support comparative analysis and annotation of genomes. The SEED Viewer allows you to explore the curated genomes that have been produced by a cooperative effort that includes Fellowship for Interpretation of Genomes (FIG), Argonne National Laboratory, the University of Chicago and teams from a number of other institutions. These pages will cover the usage of the different pages within the Seed Viewer. === Home === The home page of the seedviewer offers you several entry points to explore the data in the [[Home_of_the_SEED|SEED]]. [[Image:Home.png]] === Subsystem Select === === Subsystems === === Functional Role === === FigFams === === Annotation === === Evidence === === Blast === === Sequence === === Browse Genome === === Organism Select === === Organism Overview === === Kegg === 808f31b1960761d34fe45e9b5b5f0bb28138fbda 1854 1853 2008-11-18T10:51:03Z DanielaBartels 10 /* Home */ wikitext text/x-wiki The SEED is a framework to support comparative analysis and annotation of genomes. The SEED Viewer allows you to explore the curated genomes that have been produced by a cooperative effort that includes Fellowship for Interpretation of Genomes (FIG), Argonne National Laboratory, the University of Chicago and teams from a number of other institutions. These pages will cover the usage of the different pages within the Seed Viewer. === Home === The home page of the seedviewer offers you several entry points to explore the data in the [[Home_of_the_SEED|SEED]]. Common components of a web page in the seedviewer are the following: 1) [[Menu|The menu]] 2) [[Find Window|Find]] 3) [[Login Box|Login]] 4) Body of the Page [[Image:Home.png]] === Subsystem Select === === Subsystems === === Functional Role === === FigFams === === Annotation === === Evidence === === Blast === === Sequence === === Browse Genome === === Organism Select === === Organism Overview === === Kegg === 763d5fe4a9e618cb120507a8e0d6604e924f86ba 1856 1854 2008-11-18T10:59:27Z DanielaBartels 10 /* Home */ wikitext text/x-wiki The SEED is a framework to support comparative analysis and annotation of genomes. The SEED Viewer allows you to explore the curated genomes that have been produced by a cooperative effort that includes Fellowship for Interpretation of Genomes (FIG), Argonne National Laboratory, the University of Chicago and teams from a number of other institutions. These pages will cover the usage of the different pages within the Seed Viewer. === Home === The home page of the seedviewer offers you several entry points to explore the data in the [[Home_of_the_SEED|SEED]]. Common components of a web page in the seedviewer are the following: 1) [[Menu|The menu]] 2) [[Find Window|Find]] 3) [[Login Box|Login]] 4) Body of the Page [[Image:Home1.png]] === Subsystem Select === === Subsystems === === Functional Role === === FigFams === === Annotation === === Evidence === === Blast === === Sequence === === Browse Genome === === Organism Select === === Organism Overview === === Kegg === f8a905fa01f5c067bc6325abde7519bd1960fc19 1857 1856 2008-11-18T11:06:48Z DanielaBartels 10 /* Home */ wikitext text/x-wiki The SEED is a framework to support comparative analysis and annotation of genomes. The SEED Viewer allows you to explore the curated genomes that have been produced by a cooperative effort that includes Fellowship for Interpretation of Genomes (FIG), Argonne National Laboratory, the University of Chicago and teams from a number of other institutions. These pages will cover the usage of the different pages within the Seed Viewer. === Home === The home page of the seedviewer offers you several entry points to explore the data in the [[Home_of_the_SEED|SEED]]. Common components of a web page in the seedviewer are the following: 1) [[Menu|The menu]] Hovering over the menu will show you submenus that are relevant for the page you are viewing. The categories '''Navigate''' and '''Help''' will always be present on each page. Other menu categories are added dependent on the context of the page. Click [[Menu|here]] to learn more about using the menu. 2) [[Find Window|Find]] The Find window allows you to search for keywords or ids. To learn more about the find window, click [[here|Find]]. 3) [[Login Box|Login]] 4) Body of the Page [[Image:Home1.png]] === Subsystem Select === === Subsystems === === Functional Role === === FigFams === === Annotation === === Evidence === === Blast === === Sequence === === Browse Genome === === Organism Select === === Organism Overview === === Kegg === c728e4c831054987573e43cdac03cdd8de5b0c23 1858 1857 2008-11-18T11:13:14Z DanielaBartels 10 /* Home */ wikitext text/x-wiki The SEED is a framework to support comparative analysis and annotation of genomes. The SEED Viewer allows you to explore the curated genomes that have been produced by a cooperative effort that includes Fellowship for Interpretation of Genomes (FIG), Argonne National Laboratory, the University of Chicago and teams from a number of other institutions. These pages will cover the usage of the different pages within the Seed Viewer. === Home === The home page of the seedviewer offers you several entry points to explore the data in the [[Home_of_the_SEED|SEED]]. Common components of a web page in the seedviewer are the following: 1) [[Menu|The menu]] Hovering over the menu will show you submenus that are relevant for the page you are viewing. The categories '''Navigate''' and '''Help''' will always be present on each page. Other menu categories are added dependent on the context of the page. Click [[Menu|here]] to learn more about using the menu. 2) [[Find Window|Find]] The Find window allows you to search for keywords or ids. To learn more about the find window, click [[here|Find]]. 3) [[Login Box|Login]] Some actions may require a user to get a user account and log in. This is necessary for viewing private organisms a user has uploaded to the [[RAST|RAST_Tutorial]]. You can create a login by clicking on '''Register''' in the '''Help''' menu. To learn more about user management click [[here|UserManagement]]. 4) Body of the Page [[Image:Home1.png]] === Subsystem Select === === Subsystems === === Functional Role === === FigFams === === Annotation === === Evidence === === Blast === === Sequence === === Browse Genome === === Organism Select === === Organism Overview === === Kegg === f83275cf74b8106e62fe21ce2828f17836a594dc 1859 1858 2008-11-18T11:14:14Z DanielaBartels 10 /* Home */ wikitext text/x-wiki The SEED is a framework to support comparative analysis and annotation of genomes. The SEED Viewer allows you to explore the curated genomes that have been produced by a cooperative effort that includes Fellowship for Interpretation of Genomes (FIG), Argonne National Laboratory, the University of Chicago and teams from a number of other institutions. These pages will cover the usage of the different pages within the Seed Viewer. === Home === The home page of the seedviewer offers you several entry points to explore the data in the [[Home_of_the_SEED|SEED]]. Common components of a web page in the seedviewer are the following: 1) [[Menu|The menu]] Hovering over the menu will show you submenus that are relevant for the page you are viewing. The categories '''Navigate''' and '''Help''' will always be present on each page. Other menu categories are added dependent on the context of the page. Click [[Menu|here]] to learn more about using the menu. 2) [[Find|Find Window]] The Find window allows you to search for keywords or ids. To learn more about the find window, click [[here|Find]]. 3) [[Login|Login Box]] Some actions may require a user to get a user account and log in. This is necessary for viewing private organisms a user has uploaded to the [[RAST|RAST_Tutorial]]. You can create a login by clicking on '''Register''' in the '''Help''' menu. To learn more about user management click [[UserManagement|here]]. 4) Body of the Page [[Image:Home1.png]] === Subsystem Select === === Subsystems === === Functional Role === === FigFams === === Annotation === === Evidence === === Blast === === Sequence === === Browse Genome === === Organism Select === === Organism Overview === === Kegg === cc1bc874c8e0455bc06048099b5f93a564c78299 1860 1859 2008-11-18T11:15:20Z DanielaBartels 10 wikitext text/x-wiki The SEED is a framework to support comparative analysis and annotation of genomes. The SEED Viewer allows you to explore the curated genomes that have been produced by a cooperative effort that includes Fellowship for Interpretation of Genomes (FIG), Argonne National Laboratory, the University of Chicago and teams from a number of other institutions. These pages will cover the usage of the different pages within the Seed Viewer. === Home === The home page of the seedviewer offers you several entry points to explore the data in the [[Home_of_the_SEED|SEED]]. Common components of a web page in the seedviewer are the following: 1) [[Menu|The menu]] Hovering over the menu will show you submenus that are relevant for the page you are viewing. The categories '''Navigate''' and '''Help''' will always be present on each page. Other menu categories are added dependent on the context of the page. Click [[Menu|here]] to learn more about using the menu. 2) [[Find|Find Window]] The Find window allows you to search for keywords or ids. To learn more about the find window, click [[here|Find]]. 3) [[Login|Login Box]] Some actions may require a user to get a user account and log in. This is necessary for viewing private organisms a user has uploaded to the [[RAST|RAST_Tutorial]]. You can create a login by clicking on '''Register''' in the '''Help''' menu. To learn more about user management click [[UserManagement|here]]. 4) Body of the Page [[Image:Home1.png]] 771e8f3cfc119839a1180e41c1783e1ea65998cf 1862 1860 2008-11-18T11:17:13Z DanielaBartels 10 /* Home */ wikitext text/x-wiki The SEED is a framework to support comparative analysis and annotation of genomes. The SEED Viewer allows you to explore the curated genomes that have been produced by a cooperative effort that includes Fellowship for Interpretation of Genomes (FIG), Argonne National Laboratory, the University of Chicago and teams from a number of other institutions. These pages will cover the usage of the different pages within the Seed Viewer. === Home === The home page of the seedviewer offers you several entry points to explore the data in the [[Home_of_the_SEED|SEED]]. Common components of a web page in the seedviewer are the following: 1) [[SEED_Viewer_Manual/Menu|The menu]] Hovering over the menu will show you submenus that are relevant for the page you are viewing. The categories '''Navigate''' and '''Help''' will always be present on each page. Other menu categories are added dependent on the context of the page. Click [[SEED_Viewer_Manual/Menu|here]] to learn more about using the menu. 2) [[SEED_Viewer_Manual/Find|Find Window]] The Find window allows you to search for keywords or ids. To learn more about the find window, click [[SEED_Viewer_Manual/Find|here]]. 3) [[Login|Login Box]] Some actions may require a user to get a user account and log in. This is necessary for viewing private organisms a user has uploaded to the [[RAST|RAST_Tutorial]]. You can create a login by clicking on '''Register''' in the '''Help''' menu. To learn more about user management click [[SEED_Viewer_Manual/UserManagement|here]]. 4) Body of the Page [[Image:Home1.png]] 150b79e5f3c64dbad8b70e2b785d665d9c28d13b 1863 1862 2008-11-18T11:17:44Z DanielaBartels 10 /* Home */ wikitext text/x-wiki The SEED is a framework to support comparative analysis and annotation of genomes. The SEED Viewer allows you to explore the curated genomes that have been produced by a cooperative effort that includes Fellowship for Interpretation of Genomes (FIG), Argonne National Laboratory, the University of Chicago and teams from a number of other institutions. These pages will cover the usage of the different pages within the Seed Viewer. === Home === The home page of the seedviewer offers you several entry points to explore the data in the [[Home_of_the_SEED|SEED]]. Common components of a web page in the seedviewer are the following: 1) [[SEED_Viewer_Manual/Menu|The menu]] Hovering over the menu will show you submenus that are relevant for the page you are viewing. The categories '''Navigate''' and '''Help''' will always be present on each page. Other menu categories are added dependent on the context of the page. Click [[SEED_Viewer_Manual/Menu|here]] to learn more about using the menu. 2) [[SEED_Viewer_Manual/Find|Find Window]] The Find window allows you to search for keywords or ids. To learn more about the find window, click [[SEED_Viewer_Manual/Find|here]]. 3) [[Login|Login Box]] Some actions may require a user to get a user account and log in. This is necessary for viewing private organisms a user has uploaded to the [[RAST_Tutorial|RAST]]. You can create a login by clicking on '''Register''' in the '''Help''' menu. To learn more about user management click [[SEED_Viewer_Manual/UserManagement|here]]. 4) Body of the Page [[Image:Home1.png]] c0d824286146f241aef4dd01781a876ecdaf8259 1864 1863 2008-11-18T11:29:28Z DanielaBartels 10 /* Home */ wikitext text/x-wiki The SEED is a framework to support comparative analysis and annotation of genomes. The SEED Viewer allows you to explore the curated genomes that have been produced by a cooperative effort that includes Fellowship for Interpretation of Genomes (FIG), Argonne National Laboratory, the University of Chicago and teams from a number of other institutions. These pages will cover the usage of the different pages within the Seed Viewer. === Home === The home page of the seedviewer offers you several entry points to explore the data in the [[Home_of_the_SEED|SEED]]. Common components of a web page in the seedviewer are the following: (1) [[SEED_Viewer_Manual/Menu|The menu]] Hovering over the menu will show you submenus that are relevant for the page you are viewing. The categories '''Navigate''' and '''Help''' will always be present on each page. Other menu categories are added dependent on the context of the page. Click [[SEED_Viewer_Manual/Menu|here]] to learn more about using the menu. (2) [[SEED_Viewer_Manual/Find|Find Window]] The Find window allows you to search for keywords or ids. To learn more about the find window, click [[SEED_Viewer_Manual/Find|here]]. (3) [[WebComponents/Login|Login Box]] Some actions may require a user to get a user account and log in. This is necessary for viewing private organisms a user has uploaded to the [[RAST_Tutorial|RAST]]. You can create a login by clicking on '''Register''' in the '''Help''' menu. To learn more about user management click [[SEED_Viewer_Manual/UserManagement|here]]. (4) Body of the Page The home page allows you to specifically search the SEED data using five categories. They are presented in a [[WebComponents/Tabview|Tabview]] at the bottom of the Home page: a) Organisms Select an organism of interest in the [[SEED_Viewer_Manual/Organism Selects]] and press the button '''select'''. This will lead to the [[SEED_Viewer_Manual/OrganismPage|Organism Page]] of that organism. [[Image:Home1.png]] 7f6559f87a7a4da080f542fbd2b16f9a888a708e 1865 1864 2008-11-18T11:34:01Z DanielaBartels 10 /* Home */ wikitext text/x-wiki The SEED is a framework to support comparative analysis and annotation of genomes. The SEED Viewer allows you to explore the curated genomes that have been produced by a cooperative effort that includes Fellowship for Interpretation of Genomes (FIG), Argonne National Laboratory, the University of Chicago and teams from a number of other institutions. These pages will cover the usage of the different pages within the Seed Viewer. == Home == The home page of the seedviewer offers you several entry points to explore the data in the [[Home_of_the_SEED|SEED]]. Common components of a web page in the seedviewer are the following. The image below depicts the locations of the components: === (1) [[SEED_Viewer_Manual/Menu|The menu]] === Hovering over the menu will show you submenus that are relevant for the page you are viewing. The categories '''Navigate''' and '''Help''' will always be present on each page. Other menu categories are added dependent on the context of the page. Click [[SEED_Viewer_Manual/Menu|here]] to learn more about using the menu. === (2) [[SEED_Viewer_Manual/Find|Find Window]] === The Find window allows you to search for keywords or ids. To learn more about the find window, click [[SEED_Viewer_Manual/Find|here]]. === (3) [[WebComponents/Login|Login Box]] === Some actions may require a user to get a user account and log in. This is necessary for viewing private organisms a user has uploaded to the [[RAST_Tutorial|RAST]]. You can create a login by clicking on '''Register''' in the '''Help''' menu. To learn more about user management click [[SEED_Viewer_Manual/UserManagement|here]]. === (4) Body of the Page === The home page allows you to specifically search the SEED data using five categories. They are presented in a [[WebComponents/Tabview|Tabview]] at the bottom of the Home page: '''a) Organisms''' Select an organism of interest in the [[SEED_Viewer_Manual/Organism Selects]] and press the button '''select'''. This will lead to the [[SEED_Viewer_Manual/OrganismPage|Organism Page]] of that organism. [[Image:Home1.png]] f9facda854577c323a304d394f9a6a4478718e29 1866 1865 2008-11-18T11:50:14Z DanielaBartels 10 /* (4) Body of the Page */ wikitext text/x-wiki The SEED is a framework to support comparative analysis and annotation of genomes. The SEED Viewer allows you to explore the curated genomes that have been produced by a cooperative effort that includes Fellowship for Interpretation of Genomes (FIG), Argonne National Laboratory, the University of Chicago and teams from a number of other institutions. These pages will cover the usage of the different pages within the Seed Viewer. == Home == The home page of the seedviewer offers you several entry points to explore the data in the [[Home_of_the_SEED|SEED]]. Common components of a web page in the seedviewer are the following. The image below depicts the locations of the components: === (1) [[SEED_Viewer_Manual/Menu|The menu]] === Hovering over the menu will show you submenus that are relevant for the page you are viewing. The categories '''Navigate''' and '''Help''' will always be present on each page. Other menu categories are added dependent on the context of the page. Click [[SEED_Viewer_Manual/Menu|here]] to learn more about using the menu. === (2) [[SEED_Viewer_Manual/Find|Find Window]] === The Find window allows you to search for keywords or ids. To learn more about the find window, click [[SEED_Viewer_Manual/Find|here]]. === (3) [[WebComponents/Login|Login Box]] === Some actions may require a user to get a user account and log in. This is necessary for viewing private organisms a user has uploaded to the [[RAST_Tutorial|RAST]]. You can create a login by clicking on '''Register''' in the '''Help''' menu. To learn more about user management click [[SEED_Viewer_Manual/UserManagement|here]]. === (4) Body of the Page === The home page allows you to specifically search the SEED data using five categories. They are presented in a [[WebComponents/Tabview|Tabview]] at the bottom of the Home page: '''a) Organisms''' Select an organism of interest in the [[SEED_Viewer_Manual/OrganismSelect|Organism Select]] and press the button '''select'''. This will lead to the [[SEED_Viewer_Manual/OrganismPage|Organism Page]] of that organism. '''b) Subsystems''' Selecting a subsystem in the Select Box and clicking '''Select''' will lead you to a [[SEED_Viewer_Manual/Subsystems|Subsystem Page]]. You can narrow the selection by typing in a part of the subsystem name into the field on top of the select box. '''c) ID search''' If you know the ID of a gene or protein you're interested in, you can directly type it into this field and press '''ID Search'''. The ID can be a SEED (fig) id as well as many other types of IDs from other databases (e.g. GenBank, KEGG, SwissProt, UniProt and others). These IDs are saved in the SEED as [[Aliases|Aliases]]. [[Image:Home1.png]] 6ff89bf4ec5b48d61b4ea9b9e211c921c7edb2f8 1867 1866 2008-11-18T11:57:59Z DanielaBartels 10 wikitext text/x-wiki The SEED is a framework to support comparative analysis and annotation of genomes. The SEED Viewer allows you to explore the curated genomes that have been produced by a cooperative effort that includes Fellowship for Interpretation of Genomes (FIG), Argonne National Laboratory, the University of Chicago and teams from a number of other institutions. These pages will cover the usage of the different pages within the Seed Viewer. == Home == The home page of the seedviewer offers you several entry points to explore the data in the [[Home_of_the_SEED|SEED]]. Common components of a web page in the seedviewer are the following. The image below depicts the locations of the components: === (1) [[SEED_Viewer_Manual/Menu|The menu]] === Hovering over the menu will show you submenus that are relevant for the page you are viewing. The categories '''Navigate''' and '''Help''' will always be present on each page. Other menu categories are added dependent on the context of the page. Click [[SEED_Viewer_Manual/Menu|here]] to learn more about using the menu. === (2) [[SEED_Viewer_Manual/Find|Find Window]] === The Find window allows you to search for keywords or ids. To learn more about the find window, click [[SEED_Viewer_Manual/Find|here]]. === (3) [[WebComponents/Login|Login Box]] === Some actions may require a user to get a user account and log in. This is necessary for viewing private organisms a user has uploaded to the [[RAST_Tutorial|RAST]]. You can create a login by clicking on '''Register''' in the '''Help''' menu. To learn more about user management click [[SEED_Viewer_Manual/UserManagement|here]]. === (4) Body of the Page === The home page allows you to specifically search the SEED data using five categories. They are presented in a [[WebComponents/Tabview|Tabview]] at the bottom of the Home page: '''a) Organisms''' Select an organism of interest in the [[SEED_Viewer_Manual/OrganismSelect|Organism Select]] and press the button '''select'''. This will lead to the [[SEED_Viewer_Manual/OrganismPage|Organism Page]] of that organism. '''b) Subsystems''' Selecting a subsystem in the Select Box and clicking '''Select''' will lead you to a [[SEED_Viewer_Manual/Subsystems|Subsystem Page]]. You can narrow the selection by typing in a part of the subsystem name into the field on top of the select box. '''c) ID search''' If you know the ID of a gene or protein you're interested in, you can directly type it into this field and press '''ID Search'''. The ID can be a SEED (fig) id as well as many other types of IDs from other databases (e.g. GenBank, KEGG, SwissProt, UniProt and others). These IDs are saved in the SEED as [[Aliases|Aliases]]. '''d) Text search''' You can search for any type of data in this field. This includes search for Organisms, Subsystems, IDs as well as Functional Roles of proteins. It should be used carefully, as the search is an ---infix--- search and can take very long (e.g. if you only type in one letter it may take forever). If you already know that you are looking for example for a subsystem, it would be faster to use the Subsystems tab. '''e) BLAST''' This tab offers the option to search a DNA or protein sequence against an organism in the SEED. It is described in more detail [[SEED_Viewer_Manual/BLASTOrganism|here]]. [[Image:Home1.png]] ac90aa0655eb969a30f4fa3518c0504147563fb1 1868 1867 2008-11-18T12:00:07Z DanielaBartels 10 wikitext text/x-wiki The SEED is a framework to support comparative analysis and annotation of genomes. The SEED Viewer allows you to explore the curated genomes that have been produced by a cooperative effort that includes Fellowship for Interpretation of Genomes (FIG), Argonne National Laboratory, the University of Chicago and teams from a number of other institutions. These pages will cover the usage of the different pages within the Seed Viewer. == Home == The home page of the seedviewer offers you several entry points to explore the data in the [[Home_of_the_SEED|SEED]]. Common components of a web page in the seedviewer are the following. The image below depicts the locations of the components: === (1) [[SEED_Viewer_Manual/Menu|The menu]] === Hovering over the menu will show you submenus that are relevant for the page you are viewing. The categories '''Navigate''' and '''Help''' will always be present on each page. Other menu categories are added dependent on the context of the page. Click [[SEED_Viewer_Manual/Menu|here]] to learn more about using the menu. === (2) [[SEED_Viewer_Manual/Find|Find Window]] === The Find window allows you to search for keywords or ids. To learn more about the find window, click [[SEED_Viewer_Manual/Find|here]]. === (3) [[WebComponents/Login|Login Box]] === Some actions may require a user to get a user account and log in. This is necessary for viewing private organisms a user has uploaded to the [[RAST_Tutorial|RAST]]. You can create a login by clicking on '''Register''' in the '''Help''' menu. To learn more about user management click [[SEED_Viewer_Manual/UserManagement|here]]. === (4) Body of the Page === The home page allows you to specifically search the SEED data using five categories. They are presented in a [[WebComponents/Tabview|Tabview]] at the bottom of the Home page: '''a) Organisms''' Select an organism of interest in the [[SEED_Viewer_Manual/OrganismSelect|Organism Select]] and press the button '''select'''. This will lead to the [[SEED_Viewer_Manual/OrganismPage|Organism Page]] of that organism. '''b) Subsystems''' Selecting a subsystem in the Select Box and clicking '''Select''' will lead you to a [[SEED_Viewer_Manual/Subsystems|Subsystem Page]]. You can narrow the selection by typing in a part of the subsystem name into the field on top of the select box. '''c) ID search''' If you know the ID of a gene or protein you're interested in, you can directly type it into this field and press '''ID Search'''. The ID can be a SEED (fig) id as well as many other types of IDs from other databases (e.g. GenBank, KEGG, SwissProt, UniProt and others). These IDs are saved in the SEED as [[Aliases|Aliases]]. '''d) Text search''' You can search for any type of data in this field. This includes search for Organisms, Subsystems, IDs as well as Functional Roles of proteins. It should be used carefully, as the search is an infix search and can take very long (e.g. if you only type in one letter it may take forever). If you already know that you are looking for, e.g. a subsystem, it would be faster to use the Subsystems tab. '''e) BLAST''' This tab offers the option to search a DNA or protein sequence against an organism in the SEED. It is described in more detail [[SEED_Viewer_Manual/BLASTOrganism|here]]. [[Image:Home1.png]] 0100a223043b70fb07a94dbf7bb82e4e060768fa 1869 1868 2008-11-18T12:03:19Z DanielaBartels 10 wikitext text/x-wiki The SEED is a framework to support comparative analysis and annotation of genomes. The SEED Viewer allows you to explore the curated genomes that have been produced by a cooperative effort that includes Fellowship for Interpretation of Genomes (FIG), Argonne National Laboratory, the University of Chicago and teams from a number of other institutions. These pages will cover the usage of the different pages within the Seed Viewer. An overview of the main pages in the SeedViewer can be found [[SEED_Viewer_Manual/Contents|here]]. == Home == The home page of the seedviewer offers you several entry points to explore the data in the [[Home_of_the_SEED|SEED]]. Common components of a web page in the seedviewer are the following. The image below depicts the locations of the components: === (1) [[SEED_Viewer_Manual/Menu|The menu]] === Hovering over the menu will show you submenus that are relevant for the page you are viewing. The categories '''Navigate''' and '''Help''' will always be present on each page. Other menu categories are added dependent on the context of the page. Click [[SEED_Viewer_Manual/Menu|here]] to learn more about using the menu. === (2) [[SEED_Viewer_Manual/Find|Find Window]] === The Find window allows you to search for keywords or ids. To learn more about the find window, click [[SEED_Viewer_Manual/Find|here]]. === (3) [[WebComponents/Login|Login Box]] === Some actions may require a user to get a user account and log in. This is necessary for viewing private organisms a user has uploaded to the [[RAST_Tutorial|RAST]]. You can create a login by clicking on '''Register''' in the '''Help''' menu. To learn more about user management click [[SEED_Viewer_Manual/UserManagement|here]]. === (4) Body of the Page === The home page allows you to specifically search the SEED data using five categories. They are presented in a [[WebComponents/Tabview|Tabview]] at the bottom of the Home page: '''a) Organisms''' Select an organism of interest in the [[SEED_Viewer_Manual/OrganismSelect|Organism Select]] and press the button '''select'''. This will lead to the [[SEED_Viewer_Manual/OrganismPage|Organism Page]] of that organism. '''b) Subsystems''' Selecting a subsystem in the Select Box and clicking '''Select''' will lead you to a [[SEED_Viewer_Manual/Subsystems|Subsystem Page]]. You can narrow the selection by typing in a part of the subsystem name into the field on top of the select box. '''c) ID search''' If you know the ID of a gene or protein you're interested in, you can directly type it into this field and press '''ID Search'''. The ID can be a SEED (fig) id as well as many other types of IDs from other databases (e.g. GenBank, KEGG, SwissProt, UniProt and others). These IDs are saved in the SEED as [[Aliases|Aliases]]. '''d) Text search''' You can search for any type of data in this field. This includes search for Organisms, Subsystems, IDs as well as Functional Roles of proteins. It should be used carefully, as the search is an infix search and can take very long (e.g. if you only type in one letter it may take forever). If you already know that you are looking for, e.g. a subsystem, it would be faster to use the Subsystems tab. '''e) BLAST''' This tab offers the option to search a DNA or protein sequence against an organism in the SEED. It is described in more detail [[SEED_Viewer_Manual/BLASTOrganism|here]]. [[Image:Home1.png]] 5a01366ded96d808c56b53a1ff383f3a97663476 1870 1869 2008-11-18T12:04:19Z DanielaBartels 10 wikitext text/x-wiki The SEED is a framework to support comparative analysis and annotation of genomes. The SEED Viewer allows you to explore the curated genomes that have been produced by a cooperative effort that includes Fellowship for Interpretation of Genomes (FIG), Argonne National Laboratory, the University of Chicago and teams from a number of other institutions. These pages will cover the usage of the different pages within the Seed Viewer. An overview of the main pages in the SeedViewer can be found in the '''[[SEED_Viewer_Manual/Contents|Contents Page]]'''. == Home == The home page of the seedviewer offers you several entry points to explore the data in the [[Home_of_the_SEED|SEED]]. Common components of a web page in the seedviewer are the following. The image below depicts the locations of the components: === (1) [[SEED_Viewer_Manual/Menu|The menu]] === Hovering over the menu will show you submenus that are relevant for the page you are viewing. The categories '''Navigate''' and '''Help''' will always be present on each page. Other menu categories are added dependent on the context of the page. Click [[SEED_Viewer_Manual/Menu|here]] to learn more about using the menu. === (2) [[SEED_Viewer_Manual/Find|Find Window]] === The Find window allows you to search for keywords or ids. To learn more about the find window, click [[SEED_Viewer_Manual/Find|here]]. === (3) [[WebComponents/Login|Login Box]] === Some actions may require a user to get a user account and log in. This is necessary for viewing private organisms a user has uploaded to the [[RAST_Tutorial|RAST]]. You can create a login by clicking on '''Register''' in the '''Help''' menu. To learn more about user management click [[SEED_Viewer_Manual/UserManagement|here]]. === (4) Body of the Page === The home page allows you to specifically search the SEED data using five categories. They are presented in a [[WebComponents/Tabview|Tabview]] at the bottom of the Home page: '''a) Organisms''' Select an organism of interest in the [[SEED_Viewer_Manual/OrganismSelect|Organism Select]] and press the button '''select'''. This will lead to the [[SEED_Viewer_Manual/OrganismPage|Organism Page]] of that organism. '''b) Subsystems''' Selecting a subsystem in the Select Box and clicking '''Select''' will lead you to a [[SEED_Viewer_Manual/Subsystems|Subsystem Page]]. You can narrow the selection by typing in a part of the subsystem name into the field on top of the select box. '''c) ID search''' If you know the ID of a gene or protein you're interested in, you can directly type it into this field and press '''ID Search'''. The ID can be a SEED (fig) id as well as many other types of IDs from other databases (e.g. GenBank, KEGG, SwissProt, UniProt and others). These IDs are saved in the SEED as [[Aliases|Aliases]]. '''d) Text search''' You can search for any type of data in this field. This includes search for Organisms, Subsystems, IDs as well as Functional Roles of proteins. It should be used carefully, as the search is an infix search and can take very long (e.g. if you only type in one letter it may take forever). If you already know that you are looking for, e.g. a subsystem, it would be faster to use the Subsystems tab. '''e) BLAST''' This tab offers the option to search a DNA or protein sequence against an organism in the SEED. It is described in more detail [[SEED_Viewer_Manual/BLASTOrganism|here]]. [[Image:Home1.png]] 84f6f2bb737609968d49ee8f9b43d5b9e0f038d4 6 1464 1851 2008-11-18T10:37:16Z DanielaBartels 10 wikitext text/x-wiki da39a3ee5e6b4b0d3255bfef95601890afd80709 0 1466 1861 2008-11-18T11:15:57Z DanielaBartels 10 wikitext text/x-wiki === Subsystem Select === === Subsystems === === Functional Role === === FigFams === === Annotation === === Evidence === === Blast === === Sequence === === Browse Genome === === Organism Select === === Organism Overview === === Kegg === e5e3174b386e5e154d98ec20ee24922dbac515a8 1871 1861 2008-11-18T12:06:08Z DanielaBartels 10 wikitext text/x-wiki == Main pages of the SeedViewer == ''' [[SEED_Viewer_Manual|Home Page]] ''' === Subsystem Select === === Subsystems === === Functional Role === === FigFams === === Annotation === === Evidence === === Blast === === Sequence === === Browse Genome === === Organism Select === === Organism Overview === === Kegg === c3fe937e4d65a0e87c9c7d189ad954145907d89e 0 1467 1872 2008-11-18T12:07:05Z DanielaBartels 10 wikitext text/x-wiki == Organism Page == 23d03599e49c9b4a2a5b0dc5f92449b429cf703a 0 1469 1874 2008-11-18T12:08:39Z DanielaBartels 10 wikitext text/x-wiki == Organism Select == [[Image:HomeOrgs.png]] 6524adbe162f8405aa65eda87d355dec3c959ab5 1875 1874 2008-11-18T12:09:15Z DanielaBartels 10 wikitext text/x-wiki == Organism Select == [[Image:Home_Orgs.png]] b9fcd0e31005fafbc44bf308679ad9613f9b8b51 0 1469 1876 1875 2008-11-18T12:10:10Z DanielaBartels 10 /* Organism Select */ wikitext text/x-wiki == Organism Select == [[Image:Home Orgs.png]] 1c96b49341e44c3e677ea4438f70b0d9c24d1390 1878 1876 2008-11-18T12:11:14Z DanielaBartels 10 wikitext text/x-wiki == Organism Select == [[Image:HomeOrgs.png]] 6524adbe162f8405aa65eda87d355dec3c959ab5 1879 1878 2008-11-18T12:14:12Z DanielaBartels 10 wikitext text/x-wiki == Organism Select == [Image:HomeOrgs.png] 8c722b4fd7a0711f179da707d12be9b94eab3fdb 1880 1879 2008-11-18T12:14:23Z DanielaBartels 10 wikitext text/x-wiki == Organism Select == [[Image:HomeOrgs.png]] 6524adbe162f8405aa65eda87d355dec3c959ab5 1904 1880 2008-11-18T14:46:32Z DanielaBartels 10 wikitext text/x-wiki == Organism Select == An Organism Select lists all organisms a user has access to. Typing into the text field on top of the component will narrow the selection of organisms. Three boxes appear on the right side that also influence which organisms are shown in the selection. '''Completeness''' refers to the genome sequence of the organism. A '''complete''' organism is usually contained in only a very small number of contigs with a decent quality (meaning not too many frameshifts). If that is not the case, but the sequence is thought to contain most of the genome sequence, it is called '''incomplete'''. Sequences that contain only parts of a genome (e.g. a BAC sequence) are called '''fragments'''. Pre-selected the Organism Select will only show the '''complete''' genomes. '''Domains''' are categories the organisms can be devided into. Next to the three domains of life which are pre-selected (Bacteria, Archaea, Eukaryota) we have added the domains Environmental Sample, Plasmid and Virus. '''sort''' - choose the way you would like to sort the genomes, pre-selected is '''alphabetical''', options are by '''genome id''' (taxonomy id) and '''phylogeny''' [[Image:HomeOrgs.png]] dbe2da2620cb8dc4daf8a5838b88629a4850062f 1905 1904 2008-11-18T14:46:48Z DanielaBartels 10 /* Organism Select */ wikitext text/x-wiki == Organism Select == An Organism Select lists all organisms a user has access to. Typing into the text field on top of the component will narrow the selection of organisms. Three boxes appear on the right side that also influence which organisms are shown in the selection. '''Completeness''' refers to the genome sequence of the organism. A '''complete''' organism is usually contained in only a very small number of contigs with a decent quality (meaning not too many frameshifts). If that is not the case, but the sequence is thought to contain most of the genome sequence, it is called '''incomplete'''. Sequences that contain only parts of a genome (e.g. a BAC sequence) are called '''fragments'''. Pre-selected the Organism Select will only show the '''complete''' genomes. '''Domains''' are categories the organisms can be devided into. Next to the three domains of life which are pre-selected (Bacteria, Archaea, Eukaryota) we have added the domains Environmental Sample, Plasmid and Virus. '''sort''' - choose the way you would like to sort the genomes, pre-selected is '''alphabetical''', options are by '''genome id''' (taxonomy id) and '''phylogeny'''. [[Image:HomeOrgs.png]] 7bff644906c3c9402d7dfdc8c0130d02489b8d53 6 1470 1877 2008-11-18T12:10:45Z DanielaBartels 10 wikitext text/x-wiki da39a3ee5e6b4b0d3255bfef95601890afd80709 6 1471 1881 2008-11-18T12:19:09Z DanielaBartels 10 wikitext text/x-wiki da39a3ee5e6b4b0d3255bfef95601890afd80709 6 1472 1882 2008-11-18T12:24:34Z DanielaBartels 10 wikitext text/x-wiki da39a3ee5e6b4b0d3255bfef95601890afd80709 0 1467 1883 1872 2008-11-18T12:25:08Z DanielaBartels 10 wikitext text/x-wiki == Organism Page == [[Image:OrgsMenuGeneral.png]] 317823751edc009cd7d5fc72dcf481e8f0d957aa 1884 1883 2008-11-18T12:32:03Z DanielaBartels 10 /* Organism Page */ wikitext text/x-wiki == Organism Page == === Menu and General Information === Two menus are added to the menu bar when visiting an organism page. These are organism specific menus and described [[SEED_Viewer_Manual/Menu|here]]. The general information about an organism include name, taxonomy id (linked to NCBI), the domain (Bacteria, Archeae or Eukaryota) as well as some information about the genome (contigs, subsystems, genes). If you click on '''click for full list''', you will find more specific information about the organism. [[Image:OrgsMenuGeneral.png]] 6b707a24e3c1772c60980581d95a6c1ab0efbd60 1885 1884 2008-11-18T12:33:59Z DanielaBartels 10 /* Menu and General Information */ wikitext text/x-wiki == Organism Page == === Menu and General Information === Two menus are added to the menu bar when visiting an organism page. These are organism specific menus and described [[SEED_Viewer_Manual/Menu|here]]. The general information about an organism include name, taxonomy id (linked to NCBI), the domain (Bacteria, Archeae or Eukaryota) as well as some information about the genome (contigs, subsystems, genes). The icon next to the taxonomy id leads to a Wikipedia page for that organism (the icon only shows up if there exists a Wikipedia page). If you click on '''click for full list''', you will find more specific information about the organism. [[Image:OrgsMenuGeneral.png]] 175ace21c7281aa683b481e158003bbca3eb7386 1886 1885 2008-11-18T12:34:43Z DanielaBartels 10 /* Menu and General Information */ wikitext text/x-wiki == Organism Page == === Menu and General Information === Two menus are added to the menu bar when visiting an organism page. These are organism specific menus and described in the [[SEED_Viewer_Manual/Menu|Menu Overview]]. The general information about an organism include name, taxonomy id (linked to NCBI), the domain (Bacteria, Archeae or Eukaryota) as well as some information about the genome (contigs, subsystems, genes). The icon next to the taxonomy id leads to a Wikipedia page for that organism (the icon only shows up if there exists a Wikipedia page). If you click on '''click for full list''', you will find more specific information about the organism. [[Image:OrgsMenuGeneral.png]] 4c770aacb6da5b236549f94d1f6c1984b8da9daa 1887 1886 2008-11-18T12:43:03Z DanielaBartels 10 wikitext text/x-wiki == Organism Page == === Menu and General Information === Two menus are added to the menu bar when visiting an organism page. These are organism specific menus and described in the [[SEED_Viewer_Manual/Menu|Menu Overview]]. The general information about an organism include name, taxonomy id (linked to NCBI), the domain (Bacteria, Archeae or Eukaryota) as well as some information about the genome (contigs, subsystems, genes). The icon next to the taxonomy id leads to a Wikipedia page for that organism (the icon only shows up if there exists a Wikipedia page). If you click on '''click for full list''', you will find more specific information about the organism. [[Image:OrgsMenuGeneral.png]] === Browse, Compare and Download === The little [[WebComponents/Tabview|TabView]] next to the general information offers links to browse, compare and download the organism: '''Browse''' [[Image:OrgsBrowse.png]] '''Compare''' [[Image:OrgsCompare.png]] '''Download''' [[Image::OrgsDownload.png]] b92fa92265584e1fa84b1436a89a963ec43e5a96 1891 1887 2008-11-18T12:47:45Z DanielaBartels 10 wikitext text/x-wiki == Organism Page == === Menu and General Information === Two menus are added to the menu bar when visiting an organism page. These are organism specific menus and described in the [[SEED_Viewer_Manual/Menu|Menu Overview]]. The general information about an organism include name, taxonomy id (linked to NCBI), the domain (Bacteria, Archeae or Eukaryota) as well as some information about the genome (contigs, subsystems, genes). The icon next to the taxonomy id leads to a Wikipedia page for that organism (the icon only shows up if there exists a Wikipedia page). If you click on '''click for full list''', you will find more specific information about the organism. [[Image:OrgsMenuGeneral.png]] === Browse, Compare and Download === The little [[WebComponents/Tabview|TabView]] next to the general information offers links to browse, compare and download the organism: '''Browse''' [[Image:OrgsBrowse.png]] '''Compare''' [[Image:OrgsCompare.png]] '''Download''' [[Image:OrgsDownload.png]] 4d0a77b33d87a196c5508cfd39aa3c47e87a8efe 1892 1891 2008-11-18T13:54:27Z DanielaBartels 10 /* Browse, Compare and Download */ wikitext text/x-wiki == Organism Page == === Menu and General Information === Two menus are added to the menu bar when visiting an organism page. These are organism specific menus and described in the [[SEED_Viewer_Manual/Menu|Menu Overview]]. The general information about an organism include name, taxonomy id (linked to NCBI), the domain (Bacteria, Archeae or Eukaryota) as well as some information about the genome (contigs, subsystems, genes). The icon next to the taxonomy id leads to a Wikipedia page for that organism (the icon only shows up if there exists a Wikipedia page). If you click on '''click for full list''', you will find more specific information about the organism. [[Image:OrgsMenuGeneral.png]] === Browse, Compare and Download === The little [[WebComponents/Tabview|TabView]] next to the general information offers links to browse, compare and download the organism. These function are also available using the Organism menu. '''Browse''' Clicking the '''here''' link will lead to the [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser] for the selected organism. It lets you browse the features of your organism. [[Image:OrgsBrowse.png]] Different kinds of comparisons of your selected organism to other organisms are available here (the function-based [[SEED_Viewer_Manual/CompareMetabolicReconstruction|Compare Metabolic Reconstruction]] will enable you to see the metabolic reconstruction of your selected organism against that of another one. The sequence-based [[SEED_Viewer_Manual/MultiGenomeCompare|Multi Genome Compare]] shows a table and a graphics comparing a selected set of organisms projected against your chosen one (BLAST-based). '''Compare''' [[Image:OrgsCompare.png]] '''Download''' [[Image:OrgsDownload.png]] 71e9074ef40b036def15444f51fcead01c1f3081 1893 1892 2008-11-18T13:56:57Z DanielaBartels 10 /* Browse, Compare and Download */ wikitext text/x-wiki == Organism Page == === Menu and General Information === Two menus are added to the menu bar when visiting an organism page. These are organism specific menus and described in the [[SEED_Viewer_Manual/Menu|Menu Overview]]. The general information about an organism include name, taxonomy id (linked to NCBI), the domain (Bacteria, Archeae or Eukaryota) as well as some information about the genome (contigs, subsystems, genes). The icon next to the taxonomy id leads to a Wikipedia page for that organism (the icon only shows up if there exists a Wikipedia page). If you click on '''click for full list''', you will find more specific information about the organism. [[Image:OrgsMenuGeneral.png]] === Browse, Compare and Download === The little [[WebComponents/Tabview|TabView]] next to the general information offers links to browse, compare and download the organism. These function are also available using the Organism menu. '''Browse''' Clicking the '''here''' link will lead to the [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser] for the selected organism. It lets you browse the features of your organism. [[Image:OrgsBrowse.png]] '''Compare''' Different kinds of comparisons of your selected organism to other organisms are available here (the function-based [[SEED_Viewer_Manual/CompareMetabolicReconstruction|Compare Metabolic Reconstruction]] will enable you to see the metabolic reconstruction of your selected organism against that of another one. The sequence-based [[SEED_Viewer_Manual/MultiGenomeCompare|Multi Genome Compare]] shows a table and a graphics comparing a selected set of organisms projected against your chosen one (BLAST-based). To project the metabolic capabilities of your organism on KEGG maps, use link to the [[SEED_Viewer_Manual/KEGG|KEGG]] page. [[Image:OrgsCompare.png]] '''Download''' [[Image:OrgsDownload.png]] 8c1a5a4ae877fef231be36ae053c29f4b0e1aa3c 1894 1893 2008-11-18T14:00:09Z DanielaBartels 10 /* Browse, Compare and Download */ wikitext text/x-wiki == Organism Page == === Menu and General Information === Two menus are added to the menu bar when visiting an organism page. These are organism specific menus and described in the [[SEED_Viewer_Manual/Menu|Menu Overview]]. The general information about an organism include name, taxonomy id (linked to NCBI), the domain (Bacteria, Archeae or Eukaryota) as well as some information about the genome (contigs, subsystems, genes). The icon next to the taxonomy id leads to a Wikipedia page for that organism (the icon only shows up if there exists a Wikipedia page). If you click on '''click for full list''', you will find more specific information about the organism. [[Image:OrgsMenuGeneral.png]] === Browse, Compare and Download === The little [[WebComponents/Tabview|TabView]] next to the general information offers links to browse, compare and download the organism. These function are also available using the Organism menu. '''Browse''' Clicking the '''here''' link will lead to the [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] for the selected organism. It lets you browse the features of your organism. [[Image:OrgsBrowse.png]] '''Compare''' Different kinds of comparisons of your selected organism to other organisms are available here (the function-based [[SEED_Viewer_Manual/CompareMetabolicReconstruction|Compare Metabolic Reconstruction]] will enable you to see the metabolic reconstruction of your selected organism against that of another one. The sequence-based [[SEED_Viewer_Manual/MultiGenomeCompare|Multi Genome Compare]] shows a table and a graphics comparing a selected set of organisms projected against your chosen one (BLAST-based). To project the metabolic capabilities of your organism on KEGG maps, use link to the [[SEED_Viewer_Manual/KEGG|KEGG]] page. Blasting against your organism is enabled using the [[SEED_Viewer_Manual/BLASTOrganism|BLAST]] link. [[Image:OrgsCompare.png]] '''Download''' This tap provides a link to the [[SEED_Viewer_Manual/DownloadOrganism|Download Organism]] page. [[Image:OrgsDownload.png]] fbd51b89066c2610df33a8c8b2318d35ce490494 1895 1894 2008-11-18T14:03:33Z DanielaBartels 10 /* Organism Page */ wikitext text/x-wiki == Organism Page == === Menu and General Information === Two menus are added to the menu bar when visiting an organism page. These are organism specific menus and described in the [[SEED_Viewer_Manual/Menu|Menu Overview]]. The general information about an organism include name, taxonomy id (linked to NCBI), the domain (Bacteria, Archeae or Eukaryota) as well as some information about the genome (contigs, subsystems, genes). The icon next to the taxonomy id leads to a Wikipedia page for that organism (the icon only shows up if there exists a Wikipedia page). If you click on '''click for full list''', you will find more specific information about the organism. [[Image:OrgsMenuGeneral.png]] === Browse, Compare and Download === The little [[WebComponents/Tabview|TabView]] next to the general information offers links to browse, compare and download the organism. These function are also available using the Organism menu. '''Browse''' Clicking the '''here''' link will lead to the [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] for the selected organism. It lets you browse the features of your organism. [[Image:OrgsBrowse.png]] '''Compare''' Different kinds of comparisons of your selected organism to other organisms are available here (the function-based [[SEED_Viewer_Manual/CompareMetabolicReconstruction|Compare Metabolic Reconstruction]] will enable you to see the metabolic reconstruction of your selected organism against that of another one. The sequence-based [[SEED_Viewer_Manual/MultiGenomeCompare|Multi Genome Compare]] shows a table and a graphics comparing a selected set of organisms projected against your chosen one (BLAST-based). To project the metabolic capabilities of your organism on KEGG maps, use link to the [[SEED_Viewer_Manual/KEGG|KEGG]] page. Blasting against your organism is enabled using the [[SEED_Viewer_Manual/BLASTOrganism|BLAST]] link. [[Image:OrgsCompare.png]] '''Download''' This tap provides a link to the [[SEED_Viewer_Manual/DownloadOrganism|Download Organism]] page. [[Image:OrgsDownload.png]] == Subsystem Information == This part of the Organism Page deals with the subsystems present in your organism. The information is organized in a tab view, where the first tab shows a graphical overview of the subsystem information, while the second part lists all proteins in subsystems in a [[WebComponents/Table|Table]]. 8547da5786635f3e4a964919119aa25d65c5333f 1896 1895 2008-11-18T14:13:47Z DanielaBartels 10 /* Subsystem Information */ wikitext text/x-wiki == Organism Page == === Menu and General Information === Two menus are added to the menu bar when visiting an organism page. These are organism specific menus and described in the [[SEED_Viewer_Manual/Menu|Menu Overview]]. The general information about an organism include name, taxonomy id (linked to NCBI), the domain (Bacteria, Archeae or Eukaryota) as well as some information about the genome (contigs, subsystems, genes). The icon next to the taxonomy id leads to a Wikipedia page for that organism (the icon only shows up if there exists a Wikipedia page). If you click on '''click for full list''', you will find more specific information about the organism. [[Image:OrgsMenuGeneral.png]] === Browse, Compare and Download === The little [[WebComponents/Tabview|TabView]] next to the general information offers links to browse, compare and download the organism. These function are also available using the Organism menu. '''Browse''' Clicking the '''here''' link will lead to the [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] for the selected organism. It lets you browse the features of your organism. [[Image:OrgsBrowse.png]] '''Compare''' Different kinds of comparisons of your selected organism to other organisms are available here (the function-based [[SEED_Viewer_Manual/CompareMetabolicReconstruction|Compare Metabolic Reconstruction]] will enable you to see the metabolic reconstruction of your selected organism against that of another one. The sequence-based [[SEED_Viewer_Manual/MultiGenomeCompare|Multi Genome Compare]] shows a table and a graphics comparing a selected set of organisms projected against your chosen one (BLAST-based). To project the metabolic capabilities of your organism on KEGG maps, use link to the [[SEED_Viewer_Manual/KEGG|KEGG]] page. Blasting against your organism is enabled using the [[SEED_Viewer_Manual/BLASTOrganism|BLAST]] link. [[Image:OrgsCompare.png]] '''Download''' This tap provides a link to the [[SEED_Viewer_Manual/DownloadOrganism|Download Organism]] page. [[Image:OrgsDownload.png]] == Subsystem Information == This part of the Organism Page deals with the subsystems present in your organism. The information is organized in a tab view, where the first tab shows a graphical overview of the subsystem information, while the second part lists all proteins in subsystems in a [[WebComponents/Table|Table]]. '''(1) Graphical overview''' The leftmost bar chart (Subsystem Coverage) depicts the percentage of proteins from the selected organism that are in subsystems. In the middle the pie chart shows the distribution of subsystem categories in the organism. Hovering over the slices will inform you about the category you're looking at and the number of genes that fall in that category. [[Image:OrgsSubsystems.png]] a1150b52f618c28bb53aa60651053e9ed7851207 1898 1896 2008-11-18T14:23:55Z DanielaBartels 10 wikitext text/x-wiki == Organism Page == === Menu and General Information === Two menus are added to the menu bar when visiting an organism page. These are organism specific menus and described in the [[SEED_Viewer_Manual/Menu|Menu Overview]]. The general information about an organism include name, taxonomy id (linked to NCBI), the domain (Bacteria, Archeae or Eukaryota) as well as some information about the genome (contigs, subsystems, genes). The icon next to the taxonomy id leads to a Wikipedia page for that organism (the icon only shows up if there exists a Wikipedia page). If you click on '''click for full list''', you will find more specific information about the organism. [[Image:OrgsMenuGeneral.png]] === Browse, Compare and Download === The little [[WebComponents/Tabview|TabView]] next to the general information offers links to browse, compare and download the organism. These function are also available using the Organism menu. '''Browse''' Clicking the '''here''' link will lead to the [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] for the selected organism. It lets you browse the features of your organism. [[Image:OrgsBrowse.png]] '''Compare''' Different kinds of comparisons of your selected organism to other organisms are available here (the function-based [[SEED_Viewer_Manual/CompareMetabolicReconstruction|Compare Metabolic Reconstruction]] will enable you to see the metabolic reconstruction of your selected organism against that of another one. The sequence-based [[SEED_Viewer_Manual/MultiGenomeCompare|Multi Genome Compare]] shows a table and a graphics comparing a selected set of organisms projected against your chosen one (BLAST-based). To project the metabolic capabilities of your organism on KEGG maps, use link to the [[SEED_Viewer_Manual/KEGG|KEGG]] page. Blasting against your organism is enabled using the [[SEED_Viewer_Manual/BLASTOrganism|BLAST]] link. [[Image:OrgsCompare.png]] '''Download''' This tap provides a link to the [[SEED_Viewer_Manual/DownloadOrganism|Download Organism]] page. [[Image:OrgsDownload.png]] === Subsystem Information === This part of the Organism Page deals with the subsystems present in your organism. The information is organized in a tab view, where the first tab shows a graphical overview of the subsystem information, while the second part lists all proteins in subsystems in a [[WebComponents/Table|Table]]. '''(1) Subsystem Statistics''' The leftmost bar chart (Subsystem Coverage) depicts the percentage of proteins from the selected organism that are in subsystems. In the middle the pie chart shows the distribution of subsystem categories in the organism. Hovering over the slices will inform you about the category you're looking at and the number of genes that fall in that category. Right to the pie chart, you can find the Subsystem Feature Counts. The slices in the pie chart are presented in a tree view. Clicking the '''+''' signs will open a category and show the subcategory. Clicking the '''+''' of a subcategory will show the subsystems in that subcategory that are present in the organism. The links of the subsystems will open a [[SEED_Viewer_Manual/Subsystems|Subsystems Page]] for that subsystem. Behind all (sub)categories and subsystem you can find the number of genes that are present in the subsystem for that organism. [[Image:OrgsSubsystems.png]] '''(2) Features in Subsystems''' Click on the second tab of the tab view to get the tabular view of the Features in Subsystems. The [[WebComponents/Table|Table]] shows all the Subsystem Category, Subcategory, Subsystem Name, the Functional Role and the gene name of all features in subsystems in the organism. 63a39af920e223c00a1a2f48a3a3a0da34749ab9 1899 1898 2008-11-18T14:28:38Z DanielaBartels 10 /* Subsystem Information */ wikitext text/x-wiki == Organism Page == === Menu and General Information === Two menus are added to the menu bar when visiting an organism page. These are organism specific menus and described in the [[SEED_Viewer_Manual/Menu|Menu Overview]]. The general information about an organism include name, taxonomy id (linked to NCBI), the domain (Bacteria, Archeae or Eukaryota) as well as some information about the genome (contigs, subsystems, genes). The icon next to the taxonomy id leads to a Wikipedia page for that organism (the icon only shows up if there exists a Wikipedia page). If you click on '''click for full list''', you will find more specific information about the organism. [[Image:OrgsMenuGeneral.png]] === Browse, Compare and Download === The little [[WebComponents/Tabview|TabView]] next to the general information offers links to browse, compare and download the organism. These function are also available using the Organism menu. '''Browse''' Clicking the '''here''' link will lead to the [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] for the selected organism. It lets you browse the features of your organism. [[Image:OrgsBrowse.png]] '''Compare''' Different kinds of comparisons of your selected organism to other organisms are available here (the function-based [[SEED_Viewer_Manual/CompareMetabolicReconstruction|Compare Metabolic Reconstruction]] will enable you to see the metabolic reconstruction of your selected organism against that of another one. The sequence-based [[SEED_Viewer_Manual/MultiGenomeCompare|Multi Genome Compare]] shows a table and a graphics comparing a selected set of organisms projected against your chosen one (BLAST-based). To project the metabolic capabilities of your organism on KEGG maps, use link to the [[SEED_Viewer_Manual/KEGG|KEGG]] page. Blasting against your organism is enabled using the [[SEED_Viewer_Manual/BLASTOrganism|BLAST]] link. [[Image:OrgsCompare.png]] '''Download''' This tap provides a link to the [[SEED_Viewer_Manual/DownloadOrganism|Download Organism]] page. [[Image:OrgsDownload.png]] === Subsystem Information === This part of the Organism Page deals with the subsystems present in your organism. The information is organized in a tab view, where the first tab shows a graphical overview of the subsystem information, while the second part lists all features in subsystems in a [[WebComponents/Table|Table]]. '''(1) Subsystem Statistics''' The leftmost bar chart (Subsystem Coverage) depicts the percentage of features from the selected organism that are in subsystems. In the middle the pie chart shows the distribution of subsystem categories in the organism. Hovering over the slices will inform you about the category you're looking at and the number of genes that fall in that category. Right to the pie chart, you can find the Subsystem Feature Counts. The slices in the pie chart are presented in a tree view. Clicking the '''+''' signs will open a category and show the subcategory. Clicking the '''+''' of a subcategory will show the subsystems in that subcategory that are present in the organism. The links of the subsystems will open a [[SEED_Viewer_Manual/Subsystems|Subsystems Page]] for that subsystem. Behind all (sub)categories and subsystem you can find the number of genes that are present in the subsystem for that organism. [[Image:OrgsSubsystems.png]] '''(2) Features in Subsystems''' Click on the second tab of the tab view to get the tabular view of the Features in Subsystems. The [[WebComponents/Table|Table]] shows all the Subsystem Category, Subcategory, Subsystem Name, the Functional Role and the Feature Name of all features in subsystems in the organism. The Subsystem links again lead to the [[SEED_Viewer_Manual/Subsystems|Subsystems]] page. Functional Role links will show the [[SEED_Viewer_Manual/FunctionalRoles|Functional Role]] page for that role. Feature links go to the [[SEED_Viewer_Manual/Annotation|Annotation page]] for that feature. [[Image:OrgsFeatures.png]] 8034002a58e19268d42ea1344d6030e3f9633d9e 1901 1899 2008-11-18T14:35:25Z TobiasPaczian 17 /* Menu and General Information */ wikitext text/x-wiki == Organism Page == === Menu and General Information === Two categories are added to the menu bar when visiting an organism page. These are organism specific menus and described in the [[SEED_Viewer_Manual/Menu|Menu Overview]]. The general information about an organism include name, taxonomy id (linked to NCBI), the domain (Bacteria, Archeae or Eukaryota) as well as some information about the genome (contigs, subsystems, genes). The icon next to the taxonomy id leads to a Wikipedia page for that organism (the icon only shows up if there exists a Wikipedia page). If you click on '''click for full list''', you will find more specific information about the organism. [[Image:OrgsMenuGeneral.png]] === Browse, Compare and Download === The little [[WebComponents/Tabview|TabView]] next to the general information offers links to browse, compare and download the organism. These function are also available using the Organism menu. '''Browse''' Clicking the '''here''' link will lead to the [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] for the selected organism. It lets you browse the features of your organism. [[Image:OrgsBrowse.png]] '''Compare''' Different kinds of comparisons of your selected organism to other organisms are available here (the function-based [[SEED_Viewer_Manual/CompareMetabolicReconstruction|Compare Metabolic Reconstruction]] will enable you to see the metabolic reconstruction of your selected organism against that of another one. The sequence-based [[SEED_Viewer_Manual/MultiGenomeCompare|Multi Genome Compare]] shows a table and a graphics comparing a selected set of organisms projected against your chosen one (BLAST-based). To project the metabolic capabilities of your organism on KEGG maps, use link to the [[SEED_Viewer_Manual/KEGG|KEGG]] page. Blasting against your organism is enabled using the [[SEED_Viewer_Manual/BLASTOrganism|BLAST]] link. [[Image:OrgsCompare.png]] '''Download''' This tap provides a link to the [[SEED_Viewer_Manual/DownloadOrganism|Download Organism]] page. [[Image:OrgsDownload.png]] === Subsystem Information === This part of the Organism Page deals with the subsystems present in your organism. The information is organized in a tab view, where the first tab shows a graphical overview of the subsystem information, while the second part lists all features in subsystems in a [[WebComponents/Table|Table]]. '''(1) Subsystem Statistics''' The leftmost bar chart (Subsystem Coverage) depicts the percentage of features from the selected organism that are in subsystems. In the middle the pie chart shows the distribution of subsystem categories in the organism. Hovering over the slices will inform you about the category you're looking at and the number of genes that fall in that category. Right to the pie chart, you can find the Subsystem Feature Counts. The slices in the pie chart are presented in a tree view. Clicking the '''+''' signs will open a category and show the subcategory. Clicking the '''+''' of a subcategory will show the subsystems in that subcategory that are present in the organism. The links of the subsystems will open a [[SEED_Viewer_Manual/Subsystems|Subsystems Page]] for that subsystem. Behind all (sub)categories and subsystem you can find the number of genes that are present in the subsystem for that organism. [[Image:OrgsSubsystems.png]] '''(2) Features in Subsystems''' Click on the second tab of the tab view to get the tabular view of the Features in Subsystems. The [[WebComponents/Table|Table]] shows all the Subsystem Category, Subcategory, Subsystem Name, the Functional Role and the Feature Name of all features in subsystems in the organism. The Subsystem links again lead to the [[SEED_Viewer_Manual/Subsystems|Subsystems]] page. Functional Role links will show the [[SEED_Viewer_Manual/FunctionalRoles|Functional Role]] page for that role. Feature links go to the [[SEED_Viewer_Manual/Annotation|Annotation page]] for that feature. [[Image:OrgsFeatures.png]] 6265bae78b159a9af3e014797e2f62e7da187903 1902 1901 2008-11-18T14:38:02Z TobiasPaczian 17 /* Menu and General Information */ wikitext text/x-wiki == Organism Page == === Menu and General Information === Two categories are added to the menu bar when visiting an organism page. These are organism specific menus described in the [[SEED_Viewer_Manual/Menu|Menu Overview]]. The general information about an organism include name, taxonomy id (linked to NCBI), the domain (Bacteria, Archeae or Eukaryota) as well as some information about the genome (contigs, subsystems, genes). The icon next to the taxonomy id leads to a Wikipedia page for that organism (the icon only shows up if there exists a Wikipedia page). If you click on '''click for full list''', you will find more specific information about the organism. [[Image:OrgsMenuGeneral.png]] === Browse, Compare and Download === The little [[WebComponents/Tabview|TabView]] next to the general information offers links to browse, compare and download the organism. These function are also available using the Organism menu. '''Browse''' Clicking the '''here''' link will lead to the [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] for the selected organism. It lets you browse the features of your organism. [[Image:OrgsBrowse.png]] '''Compare''' Different kinds of comparisons of your selected organism to other organisms are available here (the function-based [[SEED_Viewer_Manual/CompareMetabolicReconstruction|Compare Metabolic Reconstruction]] will enable you to see the metabolic reconstruction of your selected organism against that of another one. The sequence-based [[SEED_Viewer_Manual/MultiGenomeCompare|Multi Genome Compare]] shows a table and a graphics comparing a selected set of organisms projected against your chosen one (BLAST-based). To project the metabolic capabilities of your organism on KEGG maps, use link to the [[SEED_Viewer_Manual/KEGG|KEGG]] page. Blasting against your organism is enabled using the [[SEED_Viewer_Manual/BLASTOrganism|BLAST]] link. [[Image:OrgsCompare.png]] '''Download''' This tap provides a link to the [[SEED_Viewer_Manual/DownloadOrganism|Download Organism]] page. [[Image:OrgsDownload.png]] === Subsystem Information === This part of the Organism Page deals with the subsystems present in your organism. The information is organized in a tab view, where the first tab shows a graphical overview of the subsystem information, while the second part lists all features in subsystems in a [[WebComponents/Table|Table]]. '''(1) Subsystem Statistics''' The leftmost bar chart (Subsystem Coverage) depicts the percentage of features from the selected organism that are in subsystems. In the middle the pie chart shows the distribution of subsystem categories in the organism. Hovering over the slices will inform you about the category you're looking at and the number of genes that fall in that category. Right to the pie chart, you can find the Subsystem Feature Counts. The slices in the pie chart are presented in a tree view. Clicking the '''+''' signs will open a category and show the subcategory. Clicking the '''+''' of a subcategory will show the subsystems in that subcategory that are present in the organism. The links of the subsystems will open a [[SEED_Viewer_Manual/Subsystems|Subsystems Page]] for that subsystem. Behind all (sub)categories and subsystem you can find the number of genes that are present in the subsystem for that organism. [[Image:OrgsSubsystems.png]] '''(2) Features in Subsystems''' Click on the second tab of the tab view to get the tabular view of the Features in Subsystems. The [[WebComponents/Table|Table]] shows all the Subsystem Category, Subcategory, Subsystem Name, the Functional Role and the Feature Name of all features in subsystems in the organism. The Subsystem links again lead to the [[SEED_Viewer_Manual/Subsystems|Subsystems]] page. Functional Role links will show the [[SEED_Viewer_Manual/FunctionalRoles|Functional Role]] page for that role. Feature links go to the [[SEED_Viewer_Manual/Annotation|Annotation page]] for that feature. [[Image:OrgsFeatures.png]] e505a003e9e47140a822ffe863e703eed51d18b3 1903 1902 2008-11-18T14:39:02Z TobiasPaczian 17 /* Menu and General Information */ wikitext text/x-wiki == Organism Page == === Menu and General Information === Two categories are added to the menu bar when visiting an organism page. These are organism specific menus described in the [[SEED_Viewer_Manual/Menu|Menu Overview]]. The general information about an organism include name, taxonomy id (linked to NCBI), the domain (Bacteria, Archeae or Eukaryota) as well as some information about the genome (contigs, subsystems, genes). The icon next to the taxonomy id leads to a Wikipedia page for that organism (the icon only shows up if there is an existing Wikipedia page). If you click on '''click for full list''', you will find more specific information about the organism. [[Image:OrgsMenuGeneral.png]] === Browse, Compare and Download === The little [[WebComponents/Tabview|TabView]] next to the general information offers links to browse, compare and download the organism. These function are also available using the Organism menu. '''Browse''' Clicking the '''here''' link will lead to the [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] for the selected organism. It lets you browse the features of your organism. [[Image:OrgsBrowse.png]] '''Compare''' Different kinds of comparisons of your selected organism to other organisms are available here (the function-based [[SEED_Viewer_Manual/CompareMetabolicReconstruction|Compare Metabolic Reconstruction]] will enable you to see the metabolic reconstruction of your selected organism against that of another one. The sequence-based [[SEED_Viewer_Manual/MultiGenomeCompare|Multi Genome Compare]] shows a table and a graphics comparing a selected set of organisms projected against your chosen one (BLAST-based). To project the metabolic capabilities of your organism on KEGG maps, use link to the [[SEED_Viewer_Manual/KEGG|KEGG]] page. Blasting against your organism is enabled using the [[SEED_Viewer_Manual/BLASTOrganism|BLAST]] link. [[Image:OrgsCompare.png]] '''Download''' This tap provides a link to the [[SEED_Viewer_Manual/DownloadOrganism|Download Organism]] page. [[Image:OrgsDownload.png]] === Subsystem Information === This part of the Organism Page deals with the subsystems present in your organism. The information is organized in a tab view, where the first tab shows a graphical overview of the subsystem information, while the second part lists all features in subsystems in a [[WebComponents/Table|Table]]. '''(1) Subsystem Statistics''' The leftmost bar chart (Subsystem Coverage) depicts the percentage of features from the selected organism that are in subsystems. In the middle the pie chart shows the distribution of subsystem categories in the organism. Hovering over the slices will inform you about the category you're looking at and the number of genes that fall in that category. Right to the pie chart, you can find the Subsystem Feature Counts. The slices in the pie chart are presented in a tree view. Clicking the '''+''' signs will open a category and show the subcategory. Clicking the '''+''' of a subcategory will show the subsystems in that subcategory that are present in the organism. The links of the subsystems will open a [[SEED_Viewer_Manual/Subsystems|Subsystems Page]] for that subsystem. Behind all (sub)categories and subsystem you can find the number of genes that are present in the subsystem for that organism. [[Image:OrgsSubsystems.png]] '''(2) Features in Subsystems''' Click on the second tab of the tab view to get the tabular view of the Features in Subsystems. The [[WebComponents/Table|Table]] shows all the Subsystem Category, Subcategory, Subsystem Name, the Functional Role and the Feature Name of all features in subsystems in the organism. The Subsystem links again lead to the [[SEED_Viewer_Manual/Subsystems|Subsystems]] page. Functional Role links will show the [[SEED_Viewer_Manual/FunctionalRoles|Functional Role]] page for that role. Feature links go to the [[SEED_Viewer_Manual/Annotation|Annotation page]] for that feature. [[Image:OrgsFeatures.png]] c17aedcc001837517230dce759fe06479aba258d 1906 1903 2008-11-18T14:48:46Z TobiasPaczian 17 /* Browse, Compare and Download */ wikitext text/x-wiki == Organism Page == === Menu and General Information === Two categories are added to the menu bar when visiting an organism page. These are organism specific menus described in the [[SEED_Viewer_Manual/Menu|Menu Overview]]. The general information about an organism include name, taxonomy id (linked to NCBI), the domain (Bacteria, Archeae or Eukaryota) as well as some information about the genome (contigs, subsystems, genes). The icon next to the taxonomy id leads to a Wikipedia page for that organism (the icon only shows up if there is an existing Wikipedia page). If you click on '''click for full list''', you will find more specific information about the organism. [[Image:OrgsMenuGeneral.png]] === Browse, Compare and Download === The little [[WebComponents/Tabview|TabView]] next to the general information offers links to browse, compare and download the organism. These function are also available using the Organism menu. '''Browse''' Clicking the '''here''' link will lead to the [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] for the selected organism. It lets you browse the features of your organism. [[Image:OrgsBrowse.png]] '''Compare''' Different kinds of comparisons of your selected organism to other organisms are available here (the function-based [[SEED_Viewer_Manual/CompareMetabolicReconstruction|Compare Metabolic Reconstruction]] will enable you to see the metabolic reconstruction of your selected organism against that of another one. The sequence-based [[SEED_Viewer_Manual/MultiGenomeCompare|Multi Genome Compare]] shows a table and a graphics comparing a selected set of organisms projected against your chosen one (BLAST-based). To project the metabolic capabilities of your organism on KEGG maps, use link to the [[SEED_Viewer_Manual/KEGG|KEGG]] page. Blasting against your organism is enabled using the [[SEED_Viewer_Manual/BLASTOrganism|BLAST]] link. [[Image:OrgsCompare.png]] '''Download''' This tab provides a link to the [[SEED_Viewer_Manual/DownloadOrganism|Download Organism]] page. [[Image:OrgsDownload.png]] === Subsystem Information === This part of the Organism Page deals with the subsystems present in your organism. The information is organized in a tab view, where the first tab shows a graphical overview of the subsystem information, while the second part lists all features in subsystems in a [[WebComponents/Table|Table]]. '''(1) Subsystem Statistics''' The leftmost bar chart (Subsystem Coverage) depicts the percentage of features from the selected organism that are in subsystems. In the middle the pie chart shows the distribution of subsystem categories in the organism. Hovering over the slices will inform you about the category you're looking at and the number of genes that fall in that category. Right to the pie chart, you can find the Subsystem Feature Counts. The slices in the pie chart are presented in a tree view. Clicking the '''+''' signs will open a category and show the subcategory. Clicking the '''+''' of a subcategory will show the subsystems in that subcategory that are present in the organism. The links of the subsystems will open a [[SEED_Viewer_Manual/Subsystems|Subsystems Page]] for that subsystem. Behind all (sub)categories and subsystem you can find the number of genes that are present in the subsystem for that organism. [[Image:OrgsSubsystems.png]] '''(2) Features in Subsystems''' Click on the second tab of the tab view to get the tabular view of the Features in Subsystems. The [[WebComponents/Table|Table]] shows all the Subsystem Category, Subcategory, Subsystem Name, the Functional Role and the Feature Name of all features in subsystems in the organism. The Subsystem links again lead to the [[SEED_Viewer_Manual/Subsystems|Subsystems]] page. Functional Role links will show the [[SEED_Viewer_Manual/FunctionalRoles|Functional Role]] page for that role. Feature links go to the [[SEED_Viewer_Manual/Annotation|Annotation page]] for that feature. [[Image:OrgsFeatures.png]] e945b04f9e8543743ba759edd4afcb9674853213 6 1473 1888 2008-11-18T12:43:25Z DanielaBartels 10 wikitext text/x-wiki da39a3ee5e6b4b0d3255bfef95601890afd80709 6 1474 1889 2008-11-18T12:44:23Z DanielaBartels 10 wikitext text/x-wiki da39a3ee5e6b4b0d3255bfef95601890afd80709 6 1475 1890 2008-11-18T12:45:11Z DanielaBartels 10 wikitext text/x-wiki da39a3ee5e6b4b0d3255bfef95601890afd80709 6 1476 1897 2008-11-18T14:14:20Z DanielaBartels 10 wikitext text/x-wiki da39a3ee5e6b4b0d3255bfef95601890afd80709 6 1477 1900 2008-11-18T14:28:58Z DanielaBartels 10 wikitext text/x-wiki da39a3ee5e6b4b0d3255bfef95601890afd80709 0 1478 1907 2008-11-18T14:50:19Z DanielaBartels 10 wikitext text/x-wiki == Menu Overview == [[Image:MenuNavigate.png]]] 67f479849a4e9599d5b65128f710209db942333b 1908 1907 2008-11-18T14:50:28Z DanielaBartels 10 wikitext text/x-wiki == Menu Overview == [[Image:MenuNavigate.png]] a1bcca7792c4a1eb6d1bb20cf5a6ca092549a643 1912 1908 2008-11-18T14:58:19Z DanielaBartels 10 /* Menu Overview */ wikitext text/x-wiki == Menu Overview == [[Image:MenuNav.png]] 365fbca06588671d40599228f883665edb3169ca 1913 1912 2008-11-18T15:00:21Z DanielaBartels 10 wikitext text/x-wiki == Menu Overview == === Navigate Menu === This menu is present on every seedviewer page. The first entry '''Startpage''' will lead to the seedviewer [[SEED_Viewer_Manual|HomePage]]. [[Image:MenuNav.png]] d3ac62265fbb9fc62b1317714af60b0f2062b396 1914 1913 2008-11-18T15:07:36Z DanielaBartels 10 /* Navigate Menu */ wikitext text/x-wiki == Menu Overview == === Navigate Menu === This menu is present on every seedviewer page. The first entry '''Startpage''' will lead to the seedviewer [[SEED_Viewer_Manual|HomePage]]. '''Organisms''' will open the [[SEED_Viewer_Manual/OrganimsSelect|Organism Select]] page. You will see an overview of all organisms in the Seed and are able to select one to view in detail. '''Subsystems''' will do the same for subsystems. '''FIGFams''' leads to an entry point for browsing [[SEED_Viewer_Manual/FIGfams|FIGfams]]. You can find more information about FIGfams [[Glossary#FIGfam|here]]. [[Image:MenuNav.png]] 99bc7123a413b2ee7c297d2b5a07e57c68effccd 1915 1914 2008-11-18T15:12:08Z DanielaBartels 10 /* Navigate Menu */ wikitext text/x-wiki == Menu Overview == === Navigate Menu === This menu is present on every seedviewer page. The first entry '''Startpage''' will lead to the seedviewer [[SEED_Viewer_Manual|HomePage]]. '''Organisms''' will open the [[SEED_Viewer_Manual/OrganimSelect|Organism Select]] page. You will see an overview of all organisms in the Seed and are able to select one to view in detail. '''Subsystems''' will do the same for subsystems. '''FIGFams''' leads to an entry point for browsing [[SEED_Viewer_Manual/FIGfams|FIGfams]]. You can find more information about FIGfams [[Glossary#FIGfam|here]]. The '''BLAST Search''' links to the [[SEED_Viewer_Manual/BLASTOrganism|BLAST Page]]. You will be able to BLAST a sequence against an organism in the SEED. [[Image:MenuNav.png]] a84382795e0bb855cca475abdab528d4665ca52e 1916 1915 2008-11-18T15:12:40Z DanielaBartels 10 /* Navigate Menu */ wikitext text/x-wiki == Menu Overview == === Navigate Menu === This menu is present on every seedviewer page. The first entry '''Startpage''' will lead to the seedviewer [[SEED_Viewer_Manual|HomePage]]. '''Organisms''' will open the [[SEED_Viewer_Manual/OrganimSelect|Organism Select]] page. You will see an overview of all organisms in the Seed and are able to select one to view in detail. '''Subsystems''' will do the same for subsystems. '''FIGFams''' leads to an entry point for browsing [[SEED_Viewer_Manual/FIGfams|FIGfams]]. You can find more information about FIGfams [[Glossary#FIGfam|here]]. The '''BLAST Search''' links to the [[SEED_Viewer_Manual/BLASTOrganism|BLAST Page]]. You will be able to BLAST a sequence against an organism in the SEED. [[Image:MenuNav.png]] === Help Menu === 97a3d7c3f46b12d5e20f2a88a20db43eda604180 1919 1916 2008-11-18T15:15:31Z DanielaBartels 10 /* Menu Overview */ wikitext text/x-wiki == Menu Overview == === Navigate Menu === This menu is present on every seedviewer page. The first entry '''Startpage''' will lead to the seedviewer [[SEED_Viewer_Manual|HomePage]]. '''Organisms''' will open the [[SEED_Viewer_Manual/OrganimSelect|Organism Select]] page. You will see an overview of all organisms in the Seed and are able to select one to view in detail. '''Subsystems''' will do the same for subsystems. '''FIGFams''' leads to an entry point for browsing [[SEED_Viewer_Manual/FIGfams|FIGfams]]. You can find more information about FIGfams [[Glossary#FIGfam|here]]. The '''BLAST Search''' links to the [[SEED_Viewer_Manual/BLASTOrganism|BLAST Page]]. You will be able to BLAST a sequence against an organism in the SEED. [[Image:MenuNav.png]] === Help Menu === [[Image:MenuHelp.png]] 156fe56d51230e686e5e58b66f5463f480c39724 1921 1919 2008-11-18T15:26:36Z DanielaBartels 10 /* Menu Overview */ wikitext text/x-wiki == Menu Overview == === Navigate Menu === This menu is present on every SeedViewer page. The first entry '''Startpage''' will lead to the seedviewer [[SEED_Viewer_Manual|HomePage]]. '''Organisms''' will open the [[SEED_Viewer_Manual/OrganimSelect|Organism Select]] page. You will see an overview of all organisms in the Seed and are able to select one to view in detail. '''Subsystems''' will do the same for subsystems. '''FIGFams''' leads to an entry point for browsing [[SEED_Viewer_Manual/FIGfams|FIGfams]]. You can find more information about FIGfams [[Glossary#FIGfam|here]]. The '''BLAST Search''' links to the [[SEED_Viewer_Manual/BLASTOrganism|BLAST Page]]. You will be able to BLAST a sequence against an organism in the SEED. [[Image:MenuNav.png]] === Help Menu === This menu is also present on all SeedViewer pages. The first link will lead you to the '''[[Home_of_the_SEED|SEED Homepage]]'''. The second link '''How to use the SEED Viewer''' leads to this wiki. [[Image:MenuHelp.png]] f2bac7c2c8ec67d3545fbf533c68af63f7ed61b1 1922 1921 2008-11-18T15:34:57Z DanielaBartels 10 /* Help Menu */ wikitext text/x-wiki == Menu Overview == === Navigate Menu === This menu is present on every SeedViewer page. The first entry '''Startpage''' will lead to the seedviewer [[SEED_Viewer_Manual|HomePage]]. '''Organisms''' will open the [[SEED_Viewer_Manual/OrganimSelect|Organism Select]] page. You will see an overview of all organisms in the Seed and are able to select one to view in detail. '''Subsystems''' will do the same for subsystems. '''FIGFams''' leads to an entry point for browsing [[SEED_Viewer_Manual/FIGfams|FIGfams]]. You can find more information about FIGfams [[Glossary#FIGfam|here]]. The '''BLAST Search''' links to the [[SEED_Viewer_Manual/BLASTOrganism|BLAST Page]]. You will be able to BLAST a sequence against an organism in the SEED. [[Image:MenuNav.png]] === Help Menu === This menu is also present on all SeedViewer pages. The first link '''What is the SEED''' will lead you to the [[Home_of_the_SEED|SEED Homepage]]. Clicking the second link '''How to use the SEED Viewer''' will get you to this wiki. '''Submitting data to SEED''' lets you browse the [[RAST_Tutorial|RAST Tutorial]]. '''Contact''' enables you to write an email to the SEED team. Clicking '''Register''' is the first step to get a user account. It will lead to the [[SEED_Viewer_Manual/Register|Register]] page. '''I forgot my password''' enables you to [[SEED_Viewer_Manual/RequestNewPassword|Request a new password]]. [[Image:MenuHelp.png]] 5595cc469a3f0e80879f94e1558efdbcaaf54bc4 1923 1922 2008-11-18T15:38:40Z DanielaBartels 10 /* Menu Overview */ wikitext text/x-wiki == Menu Overview == === Navigate Menu === This menu is present on every SeedViewer page. The first entry '''Startpage''' will lead to the seedviewer [[SEED_Viewer_Manual|HomePage]]. '''Organisms''' will open the [[SEED_Viewer_Manual/OrganimSelect|Organism Select]] page. You will see an overview of all organisms in the Seed and are able to select one to view in detail. '''Subsystems''' will do the same for subsystems. '''FIGFams''' leads to an entry point for browsing [[SEED_Viewer_Manual/FIGfams|FIGfams]]. You can find more information about FIGfams [[Glossary#FIGfam|here]]. The '''BLAST Search''' links to the [[SEED_Viewer_Manual/BLASTOrganism|BLAST Page]]. You will be able to BLAST a sequence against an organism in the SEED. [[Image:MenuNav.png]] === Help Menu === This menu is also present on all SeedViewer pages. The first link '''What is the SEED''' will lead you to the [[Home_of_the_SEED|SEED Homepage]]. Clicking the second link '''How to use the SEED Viewer''' will get you to this wiki. '''Submitting data to SEED''' lets you browse the [[RAST_Tutorial|RAST Tutorial]]. '''Contact''' enables you to write an email to the SEED team. Clicking '''Register''' is the first step to get a user account. It will lead to the [[SEED_Viewer_Manual/Register|Register]] page. '''I forgot my password''' enables you to [[SEED_Viewer_Manual/RequestNewPassword|Request a new password]]. [[Image:MenuHelp.png]] === FIGfams Menu === [[Image:MenuFIGfams.png]] c9a0a1a10cc1c40a1e2c993bffad21a163086e8f 1926 1923 2008-11-18T15:40:40Z DanielaBartels 10 /* FIGfams Menu */ wikitext text/x-wiki == Menu Overview == === Navigate Menu === This menu is present on every SeedViewer page. The first entry '''Startpage''' will lead to the seedviewer [[SEED_Viewer_Manual|HomePage]]. '''Organisms''' will open the [[SEED_Viewer_Manual/OrganimSelect|Organism Select]] page. You will see an overview of all organisms in the Seed and are able to select one to view in detail. '''Subsystems''' will do the same for subsystems. '''FIGFams''' leads to an entry point for browsing [[SEED_Viewer_Manual/FIGfams|FIGfams]]. You can find more information about FIGfams [[Glossary#FIGfam|here]]. The '''BLAST Search''' links to the [[SEED_Viewer_Manual/BLASTOrganism|BLAST Page]]. You will be able to BLAST a sequence against an organism in the SEED. [[Image:MenuNav.png]] === Help Menu === This menu is also present on all SeedViewer pages. The first link '''What is the SEED''' will lead you to the [[Home_of_the_SEED|SEED Homepage]]. Clicking the second link '''How to use the SEED Viewer''' will get you to this wiki. '''Submitting data to SEED''' lets you browse the [[RAST_Tutorial|RAST Tutorial]]. '''Contact''' enables you to write an email to the SEED team. Clicking '''Register''' is the first step to get a user account. It will lead to the [[SEED_Viewer_Manual/Register|Register]] page. '''I forgot my password''' enables you to [[SEED_Viewer_Manual/RequestNewPassword|Request a new password]]. [[Image:MenuHelp.png]] === FIGfams Menu === [[Image:MenuFIGfam.png]] 6f750517d006e84e469c3056b6589c051db0ac98 1927 1926 2008-11-18T15:45:44Z DanielaBartels 10 /* Menu Overview */ wikitext text/x-wiki == Menu Overview == === Navigate Menu === This menu is present on every SeedViewer page. The first entry '''Startpage''' will lead to the seedviewer [[SEED_Viewer_Manual|HomePage]]. '''Organisms''' will open the [[SEED_Viewer_Manual/OrganimSelect|Organism Select]] page. You will see an overview of all organisms in the Seed and are able to select one to view in detail. '''Subsystems''' will do the same for subsystems. '''FIGFams''' leads to an entry point for browsing [[SEED_Viewer_Manual/FIGfams|FIGfams]]. You can find more information about FIGfams [[Glossary#FIGfam|here]]. The '''BLAST Search''' links to the [[SEED_Viewer_Manual/BLASTOrganism|BLAST Page]]. You will be able to BLAST a sequence against an organism in the SEED. [[Image:MenuNav.png]] === Help Menu === This menu is also present on all SeedViewer pages. The first link '''What is the SEED''' will lead you to the [[Home_of_the_SEED|SEED Homepage]]. Clicking the second link '''How to use the SEED Viewer''' will get you to this wiki. '''Submitting data to SEED''' lets you browse the [[RAST_Tutorial|RAST Tutorial]]. '''Contact''' enables you to write an email to the SEED team. Clicking '''Register''' is the first step to get a user account. It will lead to the [[SEED_Viewer_Manual/Register|Register]] page. '''I forgot my password''' enables you to [[SEED_Viewer_Manual/RequestNewPassword|Request a new password]]. [[Image:MenuHelp.png]] === FIGfams Menu === On SeedViewer pages that deal with [[Glossary#FIGfam|FIGfams]], you will find an additional FIGfams menu. The '''Home''' link leads to the entry page to [[SEED_Viewer_Manual/FIGfams|FIGfams]]. The '''Release History''' will lead you to a [[SEED_Viewer_Manual/FIGfamsRelease|page]] containing a number of statistics about the current release of the FIGfams. '''Download''' will connect you to the FTP server to enable you to download the FIGfams. [[Image:MenuFIGfam.png]] 16be2752d883a543cd4d38aa94e3e0069d603ce4 6 1481 1911 2008-11-18T14:57:30Z DanielaBartels 10 wikitext text/x-wiki da39a3ee5e6b4b0d3255bfef95601890afd80709 0 1463 1917 1870 2008-11-18T15:13:47Z DanielaBartels 10 /* (1) [[SEED_Viewer_Manual/Menu|The menu]] */ wikitext text/x-wiki The SEED is a framework to support comparative analysis and annotation of genomes. The SEED Viewer allows you to explore the curated genomes that have been produced by a cooperative effort that includes Fellowship for Interpretation of Genomes (FIG), Argonne National Laboratory, the University of Chicago and teams from a number of other institutions. These pages will cover the usage of the different pages within the Seed Viewer. An overview of the main pages in the SeedViewer can be found in the '''[[SEED_Viewer_Manual/Contents|Contents Page]]'''. == Home == The home page of the seedviewer offers you several entry points to explore the data in the [[Home_of_the_SEED|SEED]]. Common components of a web page in the seedviewer are the following. The image below depicts the locations of the components: === (1) [[SEED_Viewer_Manual/Menu|The menu]] === Hovering over the menu will show you submenus that are relevant for the page you are viewing. The categories '''[[SEED_Viewer_Manual/Menu#Navigate_Menu|Navigate]]''' and '''[[SEED_Viewer_Manual/Menu#Navigate_Menu|Help]]''' will always be present on each page. Other menu categories are added dependent on the context of the page. Click [[SEED_Viewer_Manual/Menu|here]] to learn more about using the menu. === (2) [[SEED_Viewer_Manual/Find|Find Window]] === The Find window allows you to search for keywords or ids. To learn more about the find window, click [[SEED_Viewer_Manual/Find|here]]. === (3) [[WebComponents/Login|Login Box]] === Some actions may require a user to get a user account and log in. This is necessary for viewing private organisms a user has uploaded to the [[RAST_Tutorial|RAST]]. You can create a login by clicking on '''Register''' in the '''Help''' menu. To learn more about user management click [[SEED_Viewer_Manual/UserManagement|here]]. === (4) Body of the Page === The home page allows you to specifically search the SEED data using five categories. They are presented in a [[WebComponents/Tabview|Tabview]] at the bottom of the Home page: '''a) Organisms''' Select an organism of interest in the [[SEED_Viewer_Manual/OrganismSelect|Organism Select]] and press the button '''select'''. This will lead to the [[SEED_Viewer_Manual/OrganismPage|Organism Page]] of that organism. '''b) Subsystems''' Selecting a subsystem in the Select Box and clicking '''Select''' will lead you to a [[SEED_Viewer_Manual/Subsystems|Subsystem Page]]. You can narrow the selection by typing in a part of the subsystem name into the field on top of the select box. '''c) ID search''' If you know the ID of a gene or protein you're interested in, you can directly type it into this field and press '''ID Search'''. The ID can be a SEED (fig) id as well as many other types of IDs from other databases (e.g. GenBank, KEGG, SwissProt, UniProt and others). These IDs are saved in the SEED as [[Aliases|Aliases]]. '''d) Text search''' You can search for any type of data in this field. This includes search for Organisms, Subsystems, IDs as well as Functional Roles of proteins. It should be used carefully, as the search is an infix search and can take very long (e.g. if you only type in one letter it may take forever). If you already know that you are looking for, e.g. a subsystem, it would be faster to use the Subsystems tab. '''e) BLAST''' This tab offers the option to search a DNA or protein sequence against an organism in the SEED. It is described in more detail [[SEED_Viewer_Manual/BLASTOrganism|here]]. [[Image:Home1.png]] 1b525f62fec44e1ecc16bab2b9c92e00ef92d4ce 1918 1917 2008-11-18T15:14:21Z DanielaBartels 10 /* (1) [[SEED_Viewer_Manual/Menu|The menu]] */ wikitext text/x-wiki The SEED is a framework to support comparative analysis and annotation of genomes. The SEED Viewer allows you to explore the curated genomes that have been produced by a cooperative effort that includes Fellowship for Interpretation of Genomes (FIG), Argonne National Laboratory, the University of Chicago and teams from a number of other institutions. These pages will cover the usage of the different pages within the Seed Viewer. An overview of the main pages in the SeedViewer can be found in the '''[[SEED_Viewer_Manual/Contents|Contents Page]]'''. == Home == The home page of the seedviewer offers you several entry points to explore the data in the [[Home_of_the_SEED|SEED]]. Common components of a web page in the seedviewer are the following. The image below depicts the locations of the components: === (1) [[SEED_Viewer_Manual/Menu|The menu]] === Hovering over the menu will show you submenus that are relevant for the page you are viewing. The categories '''[[SEED_Viewer_Manual/Menu#Navigate_Menu|Navigate]]''' and '''[[SEED_Viewer_Manual/Menu#Help_Menu|Help]]''' will always be present on each page. Other menu categories are added dependent on the context of the page. Click [[SEED_Viewer_Manual/Menu|here]] to learn more about using the menu. === (2) [[SEED_Viewer_Manual/Find|Find Window]] === The Find window allows you to search for keywords or ids. To learn more about the find window, click [[SEED_Viewer_Manual/Find|here]]. === (3) [[WebComponents/Login|Login Box]] === Some actions may require a user to get a user account and log in. This is necessary for viewing private organisms a user has uploaded to the [[RAST_Tutorial|RAST]]. You can create a login by clicking on '''Register''' in the '''Help''' menu. To learn more about user management click [[SEED_Viewer_Manual/UserManagement|here]]. === (4) Body of the Page === The home page allows you to specifically search the SEED data using five categories. They are presented in a [[WebComponents/Tabview|Tabview]] at the bottom of the Home page: '''a) Organisms''' Select an organism of interest in the [[SEED_Viewer_Manual/OrganismSelect|Organism Select]] and press the button '''select'''. This will lead to the [[SEED_Viewer_Manual/OrganismPage|Organism Page]] of that organism. '''b) Subsystems''' Selecting a subsystem in the Select Box and clicking '''Select''' will lead you to a [[SEED_Viewer_Manual/Subsystems|Subsystem Page]]. You can narrow the selection by typing in a part of the subsystem name into the field on top of the select box. '''c) ID search''' If you know the ID of a gene or protein you're interested in, you can directly type it into this field and press '''ID Search'''. The ID can be a SEED (fig) id as well as many other types of IDs from other databases (e.g. GenBank, KEGG, SwissProt, UniProt and others). These IDs are saved in the SEED as [[Aliases|Aliases]]. '''d) Text search''' You can search for any type of data in this field. This includes search for Organisms, Subsystems, IDs as well as Functional Roles of proteins. It should be used carefully, as the search is an infix search and can take very long (e.g. if you only type in one letter it may take forever). If you already know that you are looking for, e.g. a subsystem, it would be faster to use the Subsystems tab. '''e) BLAST''' This tab offers the option to search a DNA or protein sequence against an organism in the SEED. It is described in more detail [[SEED_Viewer_Manual/BLASTOrganism|here]]. [[Image:Home1.png]] a37a3dadd9a0f27c785bb6984f9e190b55de6cdd 6 1482 1920 2008-11-18T15:17:39Z DanielaBartels 10 wikitext text/x-wiki da39a3ee5e6b4b0d3255bfef95601890afd80709 6 1483 1924 2008-11-18T15:39:01Z DanielaBartels 10 wikitext text/x-wiki da39a3ee5e6b4b0d3255bfef95601890afd80709 6 1484 1925 2008-11-18T15:40:10Z DanielaBartels 10 wikitext text/x-wiki da39a3ee5e6b4b0d3255bfef95601890afd80709 6 1485 1928 2008-11-18T15:47:40Z DanielaBartels 10 wikitext text/x-wiki da39a3ee5e6b4b0d3255bfef95601890afd80709 0 1478 1929 1927 2008-11-18T15:48:22Z DanielaBartels 10 /* Menu Overview */ wikitext text/x-wiki == Menu Overview == === Navigate Menu === This menu is present on every SeedViewer page. The first entry '''Startpage''' will lead to the seedviewer [[SEED_Viewer_Manual|HomePage]]. '''Organisms''' will open the [[SEED_Viewer_Manual/OrganimSelect|Organism Select]] page. You will see an overview of all organisms in the Seed and are able to select one to view in detail. '''Subsystems''' will do the same for subsystems. '''FIGFams''' leads to an entry point for browsing [[SEED_Viewer_Manual/FIGfams|FIGfams]]. You can find more information about FIGfams [[Glossary#FIGfam|here]]. The '''BLAST Search''' links to the [[SEED_Viewer_Manual/BLASTOrganism|BLAST Page]]. You will be able to BLAST a sequence against an organism in the SEED. [[Image:MenuNav.png]] === Help Menu === This menu is also present on all SeedViewer pages. The first link '''What is the SEED''' will lead you to the [[Home_of_the_SEED|SEED Homepage]]. Clicking the second link '''How to use the SEED Viewer''' will get you to this wiki. '''Submitting data to SEED''' lets you browse the [[RAST_Tutorial|RAST Tutorial]]. '''Contact''' enables you to write an email to the SEED team. Clicking '''Register''' is the first step to get a user account. It will lead to the [[SEED_Viewer_Manual/Register|Register]] page. '''I forgot my password''' enables you to [[SEED_Viewer_Manual/RequestNewPassword|Request a new password]]. [[Image:MenuHelp.png]] === Organism Menu === [[Image:MenuOrganism.png]] === FIGfams Menu === On SeedViewer pages that deal with [[Glossary#FIGfam|FIGfams]], you will find an additional FIGfams menu. The '''Home''' link leads to the entry page to [[SEED_Viewer_Manual/FIGfams|FIGfams]]. The '''Release History''' will lead you to a [[SEED_Viewer_Manual/FIGfamsRelease|page]] containing a number of statistics about the current release of the FIGfams. '''Download''' will connect you to the FTP server to enable you to download the FIGfams. [[Image:MenuFIGfam.png]] 4dfc99724b7afd0771abcc22fe35debf53606856 1930 1929 2008-11-18T16:06:35Z DanielaBartels 10 /* Organism Menu */ wikitext text/x-wiki == Menu Overview == === Navigate Menu === This menu is present on every SeedViewer page. The first entry '''Startpage''' will lead to the seedviewer [[SEED_Viewer_Manual|HomePage]]. '''Organisms''' will open the [[SEED_Viewer_Manual/OrganimSelect|Organism Select]] page. You will see an overview of all organisms in the Seed and are able to select one to view in detail. '''Subsystems''' will do the same for subsystems. '''FIGFams''' leads to an entry point for browsing [[SEED_Viewer_Manual/FIGfams|FIGfams]]. You can find more information about FIGfams [[Glossary#FIGfam|here]]. The '''BLAST Search''' links to the [[SEED_Viewer_Manual/BLASTOrganism|BLAST Page]]. You will be able to BLAST a sequence against an organism in the SEED. [[Image:MenuNav.png]] === Help Menu === This menu is also present on all SeedViewer pages. The first link '''What is the SEED''' will lead you to the [[Home_of_the_SEED|SEED Homepage]]. Clicking the second link '''How to use the SEED Viewer''' will get you to this wiki. '''Submitting data to SEED''' lets you browse the [[RAST_Tutorial|RAST Tutorial]]. '''Contact''' enables you to write an email to the SEED team. Clicking '''Register''' is the first step to get a user account. It will lead to the [[SEED_Viewer_Manual/Register|Register]] page. '''I forgot my password''' enables you to [[SEED_Viewer_Manual/RequestNewPassword|Request a new password]]. [[Image:MenuHelp.png]] === Organism Menu === In the context of a selected organism, an organism menu will appear. '''General Information''' will lead to the [[SEED_Viewer_Manual/OrganismPage|Organism Page]] of the selected organism. The '''Feature Table''' will open the [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] and show you the features present in that organism. '''Genome Browser''' leads to the [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] for the selected organism. Clicking '''Scenarios''' shows the [[SEED_Viewer_Manual/Scenarios|Scenarios]] page for your organism. '''Subsystems''' opens a page that lets you select subsystems. '''Export''' enables you to [[SEED_Viewer_Manual/Export|download]] the features of your organism. [[Image:MenuOrganism.png]] === Comparative Tools === This menu is also present whenever an organism is viewed. Different kinds of comparisons of your selected organism to other organisms are available here. '''Function based Comparison''' - The [[SEED_Viewer_Manual/CompareMetabolicReconstruction|Compare Metabolic Reconstruction]] will enable you to see the metabolic reconstruction of your selected organism against that of another one. The '''Sequence based Comparison [[SEED_Viewer_Manual/MultiGenomeCompare|Multi Genome Compare]] shows a table and a graphics comparing a selected set of organisms projected against your chosen one (BLAST-based). Use the '''KEGG Metabolic Analysis''' [[SEED_Viewer_Manual/KEGG|to project the metabolic capabilities]] of your organism on KEGG maps. Blasting against your organism is enabled using the '''[[SEED_Viewer_Manual/BLASTOrganism|BLAST Search]]'''. [[Image:CompTools.png]] === FIGfams Menu === On SeedViewer pages that deal with [[Glossary#FIGfam|FIGfams]], you will find an additional FIGfams menu. The '''Home''' link leads to the entry page to [[SEED_Viewer_Manual/FIGfams|FIGfams]]. The '''Release History''' will lead you to a [[SEED_Viewer_Manual/FIGfamsRelease|page]] containing a number of statistics about the current release of the FIGfams. '''Download''' will connect you to the FTP server to enable you to download the FIGfams. [[Image:MenuFIGfam.png]] 112e9297ccef3265491d192820411e455e88ad2f 1932 1930 2008-11-18T16:13:07Z DanielaBartels 10 /* Navigate Menu */ wikitext text/x-wiki == Menu Overview == === Navigate Menu === This menu is present on every SeedViewer page. The first entry '''Startpage''' will lead to the SeedViewer [[SEED_Viewer_Manual|HomePage]]. '''Organisms''' will open the [[SEED_Viewer_Manual/OrganimSelect|Organism Select]] page. You will see an overview of all organisms in the SEED and are able to select one to view in detail. '''Subsystems''' will do the same for subsystems. '''FIGFams''' leads to an entry point for browsing [[SEED_Viewer_Manual/FIGfams|FIGfams]]. You can find more information about FIGfams [[Glossary#FIGfam|here]]. The '''BLAST Search''' links to the [[SEED_Viewer_Manual/BLASTOrganism|BLAST Page]]. You will be able to BLAST a sequence against an organism in the SEED. [[Image:MenuNav.png]] === Help Menu === This menu is also present on all SeedViewer pages. The first link '''What is the SEED''' will lead you to the [[Home_of_the_SEED|SEED Homepage]]. Clicking the second link '''How to use the SEED Viewer''' will get you to this wiki. '''Submitting data to SEED''' lets you browse the [[RAST_Tutorial|RAST Tutorial]]. '''Contact''' enables you to write an email to the SEED team. Clicking '''Register''' is the first step to get a user account. It will lead to the [[SEED_Viewer_Manual/Register|Register]] page. '''I forgot my password''' enables you to [[SEED_Viewer_Manual/RequestNewPassword|Request a new password]]. [[Image:MenuHelp.png]] === Organism Menu === In the context of a selected organism, an organism menu will appear. '''General Information''' will lead to the [[SEED_Viewer_Manual/OrganismPage|Organism Page]] of the selected organism. The '''Feature Table''' will open the [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] and show you the features present in that organism. '''Genome Browser''' leads to the [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] for the selected organism. Clicking '''Scenarios''' shows the [[SEED_Viewer_Manual/Scenarios|Scenarios]] page for your organism. '''Subsystems''' opens a page that lets you select subsystems. '''Export''' enables you to [[SEED_Viewer_Manual/Export|download]] the features of your organism. [[Image:MenuOrganism.png]] === Comparative Tools === This menu is also present whenever an organism is viewed. Different kinds of comparisons of your selected organism to other organisms are available here. '''Function based Comparison''' - The [[SEED_Viewer_Manual/CompareMetabolicReconstruction|Compare Metabolic Reconstruction]] will enable you to see the metabolic reconstruction of your selected organism against that of another one. The '''Sequence based Comparison [[SEED_Viewer_Manual/MultiGenomeCompare|Multi Genome Compare]] shows a table and a graphics comparing a selected set of organisms projected against your chosen one (BLAST-based). Use the '''KEGG Metabolic Analysis''' [[SEED_Viewer_Manual/KEGG|to project the metabolic capabilities]] of your organism on KEGG maps. Blasting against your organism is enabled using the '''[[SEED_Viewer_Manual/BLASTOrganism|BLAST Search]]'''. [[Image:CompTools.png]] === FIGfams Menu === On SeedViewer pages that deal with [[Glossary#FIGfam|FIGfams]], you will find an additional FIGfams menu. The '''Home''' link leads to the entry page to [[SEED_Viewer_Manual/FIGfams|FIGfams]]. The '''Release History''' will lead you to a [[SEED_Viewer_Manual/FIGfamsRelease|page]] containing a number of statistics about the current release of the FIGfams. '''Download''' will connect you to the FTP server to enable you to download the FIGfams. [[Image:MenuFIGfam.png]] 8f9807bd4567b0a810eef531313eca77e3817f43 1933 1932 2008-11-18T16:13:30Z DanielaBartels 10 /* Navigate Menu */ wikitext text/x-wiki == Menu Overview == === Navigate Menu === This menu is present on every SeedViewer page. The first entry '''Startpage''' will lead to the SeedViewer [[SEED_Viewer_Manual|HomePage]]. '''Organisms''' will open the [[SEED_Viewer_Manual/OrganismSelect|Organism Select]] page. You will see an overview of all organisms in the SEED and are able to select one to view in detail. '''Subsystems''' will do the same for subsystems. '''FIGFams''' leads to an entry point for browsing [[SEED_Viewer_Manual/FIGfams|FIGfams]]. You can find more information about FIGfams [[Glossary#FIGfam|here]]. The '''BLAST Search''' links to the [[SEED_Viewer_Manual/BLASTOrganism|BLAST Page]]. You will be able to BLAST a sequence against an organism in the SEED. [[Image:MenuNav.png]] === Help Menu === This menu is also present on all SeedViewer pages. The first link '''What is the SEED''' will lead you to the [[Home_of_the_SEED|SEED Homepage]]. Clicking the second link '''How to use the SEED Viewer''' will get you to this wiki. '''Submitting data to SEED''' lets you browse the [[RAST_Tutorial|RAST Tutorial]]. '''Contact''' enables you to write an email to the SEED team. Clicking '''Register''' is the first step to get a user account. It will lead to the [[SEED_Viewer_Manual/Register|Register]] page. '''I forgot my password''' enables you to [[SEED_Viewer_Manual/RequestNewPassword|Request a new password]]. [[Image:MenuHelp.png]] === Organism Menu === In the context of a selected organism, an organism menu will appear. '''General Information''' will lead to the [[SEED_Viewer_Manual/OrganismPage|Organism Page]] of the selected organism. The '''Feature Table''' will open the [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] and show you the features present in that organism. '''Genome Browser''' leads to the [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] for the selected organism. Clicking '''Scenarios''' shows the [[SEED_Viewer_Manual/Scenarios|Scenarios]] page for your organism. '''Subsystems''' opens a page that lets you select subsystems. '''Export''' enables you to [[SEED_Viewer_Manual/Export|download]] the features of your organism. [[Image:MenuOrganism.png]] === Comparative Tools === This menu is also present whenever an organism is viewed. Different kinds of comparisons of your selected organism to other organisms are available here. '''Function based Comparison''' - The [[SEED_Viewer_Manual/CompareMetabolicReconstruction|Compare Metabolic Reconstruction]] will enable you to see the metabolic reconstruction of your selected organism against that of another one. The '''Sequence based Comparison [[SEED_Viewer_Manual/MultiGenomeCompare|Multi Genome Compare]] shows a table and a graphics comparing a selected set of organisms projected against your chosen one (BLAST-based). Use the '''KEGG Metabolic Analysis''' [[SEED_Viewer_Manual/KEGG|to project the metabolic capabilities]] of your organism on KEGG maps. Blasting against your organism is enabled using the '''[[SEED_Viewer_Manual/BLASTOrganism|BLAST Search]]'''. [[Image:CompTools.png]] === FIGfams Menu === On SeedViewer pages that deal with [[Glossary#FIGfam|FIGfams]], you will find an additional FIGfams menu. The '''Home''' link leads to the entry page to [[SEED_Viewer_Manual/FIGfams|FIGfams]]. The '''Release History''' will lead you to a [[SEED_Viewer_Manual/FIGfamsRelease|page]] containing a number of statistics about the current release of the FIGfams. '''Download''' will connect you to the FTP server to enable you to download the FIGfams. [[Image:MenuFIGfam.png]] 5fec772ce20107874954eb0e9eb6971817b1db75 1934 1933 2008-11-18T16:15:46Z DanielaBartels 10 /* Comparative Tools */ wikitext text/x-wiki == Menu Overview == === Navigate Menu === This menu is present on every SeedViewer page. The first entry '''Startpage''' will lead to the SeedViewer [[SEED_Viewer_Manual|HomePage]]. '''Organisms''' will open the [[SEED_Viewer_Manual/OrganismSelect|Organism Select]] page. You will see an overview of all organisms in the SEED and are able to select one to view in detail. '''Subsystems''' will do the same for subsystems. '''FIGFams''' leads to an entry point for browsing [[SEED_Viewer_Manual/FIGfams|FIGfams]]. You can find more information about FIGfams [[Glossary#FIGfam|here]]. The '''BLAST Search''' links to the [[SEED_Viewer_Manual/BLASTOrganism|BLAST Page]]. You will be able to BLAST a sequence against an organism in the SEED. [[Image:MenuNav.png]] === Help Menu === This menu is also present on all SeedViewer pages. The first link '''What is the SEED''' will lead you to the [[Home_of_the_SEED|SEED Homepage]]. Clicking the second link '''How to use the SEED Viewer''' will get you to this wiki. '''Submitting data to SEED''' lets you browse the [[RAST_Tutorial|RAST Tutorial]]. '''Contact''' enables you to write an email to the SEED team. Clicking '''Register''' is the first step to get a user account. It will lead to the [[SEED_Viewer_Manual/Register|Register]] page. '''I forgot my password''' enables you to [[SEED_Viewer_Manual/RequestNewPassword|Request a new password]]. [[Image:MenuHelp.png]] === Organism Menu === In the context of a selected organism, an organism menu will appear. '''General Information''' will lead to the [[SEED_Viewer_Manual/OrganismPage|Organism Page]] of the selected organism. The '''Feature Table''' will open the [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] and show you the features present in that organism. '''Genome Browser''' leads to the [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] for the selected organism. Clicking '''Scenarios''' shows the [[SEED_Viewer_Manual/Scenarios|Scenarios]] page for your organism. '''Subsystems''' opens a page that lets you select subsystems. '''Export''' enables you to [[SEED_Viewer_Manual/Export|download]] the features of your organism. [[Image:MenuOrganism.png]] === Comparative Tools === This menu is also present whenever an organism is viewed. Different kinds of comparisons of your selected organism to other organisms are available here. '''Function based Comparison''' - The [[SEED_Viewer_Manual/CompareMetabolicReconstruction|Compare Metabolic Reconstruction]] will enable you to see the metabolic reconstruction of your selected organism against that of another one. The '''Sequence based Comparison''' [[SEED_Viewer_Manual/MultiGenomeCompare|Multi Genome Compare]] shows a table and a graphics comparing a selected set of organisms projected against your chosen one (BLAST-based). Use the '''KEGG Metabolic Analysis''' [[SEED_Viewer_Manual/KEGG|to project the metabolic capabilities]] of your organism on KEGG maps. Blasting against your organism is enabled using the '''[[SEED_Viewer_Manual/BLASTOrganism|BLAST Search]]'''. [[Image:CompTools.png]] === FIGfams Menu === On SeedViewer pages that deal with [[Glossary#FIGfam|FIGfams]], you will find an additional FIGfams menu. The '''Home''' link leads to the entry page to [[SEED_Viewer_Manual/FIGfams|FIGfams]]. The '''Release History''' will lead you to a [[SEED_Viewer_Manual/FIGfamsRelease|page]] containing a number of statistics about the current release of the FIGfams. '''Download''' will connect you to the FTP server to enable you to download the FIGfams. [[Image:MenuFIGfam.png]] 392084057e7eebfd628a58e44b11743b6e9e6a3e 6 1486 1931 2008-11-18T16:07:52Z DanielaBartels 10 wikitext text/x-wiki da39a3ee5e6b4b0d3255bfef95601890afd80709 0 1487 1935 2008-11-18T16:19:29Z DanielaBartels 10 wikitext text/x-wiki [[Image:BlastOrg.png]] 54ba26be226fc579a16f35ba02ea726f70f901fe 1942 1935 2008-11-18T16:42:22Z DanielaBartels 10 wikitext text/x-wiki == Blast against an organism == Blasting a sequence against an organism includes two steps. First, you paste your custom sequence into the first text field. Choose nucleotide or amino acid depending on your input sequence (DNA or protein) in the '''sequence''' cell. The BLAST filter can be turned on or off in the '''filter''' cell. Choose the evalue '''cutoff''' you want to apply to the results (Hits with a larger evalue will not be shown). The '''word size''', a BLAST parameter for building the seeds of hits, can also be changed if needed. As a second step, choose the genome you want to BLAST against in the select box. Click the button '''BLAST''' if you are ready. '''Clear''' will reset all options. The output of the BLAST search will provide links of the hits into the [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]]. The region that is hit in the genome will be marked using a red box. [[Image:BlastOrg.png]] cc576e5f74846690c4ab22637d4cd0b91ac579ed 6 1488 1936 2008-11-18T16:19:57Z DanielaBartels 10 wikitext text/x-wiki da39a3ee5e6b4b0d3255bfef95601890afd80709 0 1466 1937 1871 2008-11-18T16:25:20Z DanielaBartels 10 /* Blast */ wikitext text/x-wiki == Main pages of the SeedViewer == ''' [[SEED_Viewer_Manual|Home Page]] ''' === Subsystem Select === === Subsystems === === Functional Role === === FigFams === === Annotation === === Evidence === [[SEED_Viewer_Manual/BLASTOrganism|BLAST against an organism]] === Sequence === === Browse Genome === === Organism Select === === Organism Overview === === Kegg === f6f113a602465c7cb9f96d600b2904e6d53530ea 1938 1937 2008-11-18T16:25:38Z DanielaBartels 10 /* Evidence */ wikitext text/x-wiki == Main pages of the SeedViewer == ''' [[SEED_Viewer_Manual|Home Page]] ''' === Subsystem Select === === Subsystems === === Functional Role === === FigFams === === Annotation === === Evidence === '''[[SEED_Viewer_Manual/BLASTOrganism|BLAST against an organism]]''' === Sequence === === Browse Genome === === Organism Select === === Organism Overview === === Kegg === 155bfe27d8325ba26786a4a9665542ad42235c35 1939 1938 2008-11-18T16:27:12Z DanielaBartels 10 /* Organism Overview */ wikitext text/x-wiki == Main pages of the SeedViewer == ''' [[SEED_Viewer_Manual|Home Page]] ''' === Subsystem Select === === Subsystems === === Functional Role === === FigFams === === Annotation === === Evidence === '''[[SEED_Viewer_Manual/BLASTOrganism|BLAST against an organism]]''' === Sequence === === Browse Genome === === Organism Select === '''[[SEED_Viewer_Manual/OrganismPage|Organism Page]]''' === Kegg === d03cb05e5e8ed31f682d11311b53b39d2d29c745 1940 1939 2008-11-18T16:27:47Z DanielaBartels 10 /* Organism Select */ wikitext text/x-wiki == Main pages of the SeedViewer == ''' [[SEED_Viewer_Manual|Home Page]] ''' === Subsystem Select === === Subsystems === === Functional Role === === FigFams === === Annotation === === Evidence === '''[[SEED_Viewer_Manual/BLASTOrganism|BLAST against an organism]]''' === Sequence === === Browse Genome === '''[[SEED_Viewer_Manual/OrganismSelect|Organism Select]]''' '''[[SEED_Viewer_Manual/OrganismPage|Organism Page]]''' === Kegg === 35fe3441cb01d9f77d2dda5125fcf35c5ccb4d7f 1941 1940 2008-11-18T16:29:20Z DanielaBartels 10 /* Main pages of the SeedViewer */ wikitext text/x-wiki == Main pages of the SeedViewer == ''' [[SEED_Viewer_Manual|Home Page]] ''' ''' [[SEED_Viewer_Manual|Menu]] ''' === Subsystem Select === === Subsystems === === Functional Role === === FigFams === === Annotation === === Evidence === '''[[SEED_Viewer_Manual/BLASTOrganism|BLAST against an organism]]''' === Sequence === === Browse Genome === '''[[SEED_Viewer_Manual/OrganismSelect|Organism Select]]''' '''[[SEED_Viewer_Manual/OrganismPage|Organism Page]]''' === Kegg === e38abf0177862b45cca91bfab670aaeb9f184d2e 1946 1941 2008-11-18T16:49:05Z DanielaBartels 10 /* Browse Genome */ wikitext text/x-wiki == Main pages of the SeedViewer == ''' [[SEED_Viewer_Manual|Home Page]] ''' ''' [[SEED_Viewer_Manual|Menu]] ''' === Subsystem Select === === Subsystems === === Functional Role === === FigFams === === Annotation === === Evidence === '''[[SEED_Viewer_Manual/BLASTOrganism|BLAST against an organism]]''' === Sequence === '''[[SEED_Viewer_Manual/GenomeBrowser|Browse Genome]]''' '''[[SEED_Viewer_Manual/OrganismSelect|Organism Select]]''' '''[[SEED_Viewer_Manual/OrganismPage|Organism Page]]''' === Kegg === c6aac85163c13264f1eef35984ce61576ec7d67b 1971 1946 2008-11-21T11:57:20Z DanielaBartels 10 /* Annotation */ wikitext text/x-wiki == Main pages of the SeedViewer == ''' [[SEED_Viewer_Manual|Home Page]] ''' ''' [[SEED_Viewer_Manual|Menu]] ''' === Subsystem Select === === Subsystems === === Functional Role === === FigFams === [[SEED_Viewer_Manual/Annotation|Annotation]] === Evidence === '''[[SEED_Viewer_Manual/BLASTOrganism|BLAST against an organism]]''' === Sequence === '''[[SEED_Viewer_Manual/GenomeBrowser|Browse Genome]]''' '''[[SEED_Viewer_Manual/OrganismSelect|Organism Select]]''' '''[[SEED_Viewer_Manual/OrganismPage|Organism Page]]''' === Kegg === d8a03bba57dfd4dc48979f712ebe388162636f67 1972 1971 2008-11-21T11:57:34Z DanielaBartels 10 /* FigFams */ wikitext text/x-wiki == Main pages of the SeedViewer == ''' [[SEED_Viewer_Manual|Home Page]] ''' ''' [[SEED_Viewer_Manual|Menu]] ''' === Subsystem Select === === Subsystems === === Functional Role === === FigFams === '''[[SEED_Viewer_Manual/Annotation|Annotation]]''' === Evidence === '''[[SEED_Viewer_Manual/BLASTOrganism|BLAST against an organism]]''' === Sequence === '''[[SEED_Viewer_Manual/GenomeBrowser|Browse Genome]]''' '''[[SEED_Viewer_Manual/OrganismSelect|Organism Select]]''' '''[[SEED_Viewer_Manual/OrganismPage|Organism Page]]''' === Kegg === bd4ef4244482d9c387361c28cf1acaba74d8b799 0 1489 1943 2008-11-18T16:46:30Z DanielaBartels 10 wikitext text/x-wiki == Genome Browser == [[Image:GenomeBrowser6fw]] 8ace969417a760f04af913d34f5c7de16adcfbf1 1945 1943 2008-11-18T16:48:03Z DanielaBartels 10 /* Genome Browser */ wikitext text/x-wiki == Genome Browser == [[Image:GenomeBrowser6fw.png]] 846292ab52db20862b0f28298ab3b576da513bd2 1947 1945 2008-11-18T16:52:10Z DanielaBartels 10 /* Genome Browser */ wikitext text/x-wiki == Genome Browser == [[Image:GenomeBrowserLoc.png]] [[Image:GenomeBrowserFoc.png]] [[Image:GenomeBrowserList.png]] [[Image:GenomeBrowser6fw.png]] [[Image:GenomeBrowserFeat.png]] 6e9c0a1b17981b82740a21a8ee630e3b0f9f0f3d 1949 1947 2008-11-18T16:59:46Z DanielaBartels 10 /* Genome Browser */ wikitext text/x-wiki == Genome Browser == [[Image:GenomeBrowserLoc.png]] [[Image:GenomeBrowser6fw.png]] [[Image:GenomeBrowserFeat.png]] 02d748ba96d32f74a2c2394cb2c275fe1d64674f 1951 1949 2008-11-18T17:09:38Z DanielaBartels 10 /* Genome Browser */ wikitext text/x-wiki == Genome Browser == The Genome Browser enables you to view the features of a genome in their genomic context. The six frame view represents the six reading frames for proteins. Blue arrows are printed representing protein features. Their direction depicts the strand of the protein. As RNA features have no reading frames, they can be found in the middle line of the image, represented by little blue boxes. === The six frame view === [[Image:GenomeBrowser6fw.png]] [[Image:GenomeBrowserLoc.png]] [[Image:GenomeBrowserFeat.png]] 8769fad8df48baa430a2bef14c212013cc50b829 1952 1951 2008-11-21T09:40:37Z DanielaBartels 10 /* Genome Browser */ wikitext text/x-wiki == Genome Browser == The Genome Browser enables you to view the features of a genome in their genomic context. The page is divided into three parts, a [[WebComponents/Tabview|TabView]], the Six Frame View, and a [[WebComponents/Table|table]] showing all features of an organism. === The six frame view === The six frame view represents the six reading frames for proteins (-3, -2, -1, 1, 2, 3). Blue arrows are printed representing protein features. Their direction depicts the strand of the protein (- or +). As RNA features (tRNAs, rRNAs, or other genomic features like binding sites) have no reading frames, they can be found in the middle line of the image, represented by little blue boxes. [[Image:GenomeBrowser6fw.png]] [[Image:GenomeBrowserLoc.png]] [[Image:GenomeBrowserFeat.png]] f069ebebafba21699ee4f536b540cecbfcab9249 1953 1952 2008-11-21T09:44:20Z DanielaBartels 10 /* Genome Browser */ wikitext text/x-wiki == Genome Browser == The Genome Browser enables you to view the features of a genome in their genomic context. The page is divided into three parts, a Control [[WebComponents/Tabview|TabView]], the Six Frame View, and a [[WebComponents/Table|table]] showing all features of an organism. === The Six Frame View === The six frame view represents the six reading frames for proteins (-3, -2, -1, 1, 2, 3). Blue arrows are printed representing protein features. Their direction depicts the strand of the protein (- or +). As RNA features (tRNAs, rRNAs, or other genomic features like binding sites) have no reading frames, they can be found in the middle line of the image, represented by little blue boxes. Hovering over a feature will show a tooltip containing information about the feature, including the name, the position in the genome, the [[Glossary#Functional_role|functional role]] and the [[Glossary#Subsystem|subsystem(s)] it's in. [[Image:GenomeBrowser6fw.png]] === The Control TabView === [[Image:GenomeBrowserLoc.png]] [[Image:GenomeBrowserFeat.png]] d2abcdd5d2192fb438d3d45cf1be4b85e19da84d 1954 1953 2008-11-21T09:44:51Z DanielaBartels 10 /* Genome Browser */ wikitext text/x-wiki == Genome Browser == The Genome Browser enables you to view the features of a genome in their genomic context. The page is divided into three parts, a Control [[WebComponents/Tabview|TabView]], the Six Frame View, and a [[WebComponents/Table|table]] showing all features of an organism. === The Six Frame View === The six frame view represents the six reading frames for proteins (-3, -2, -1, 1, 2, 3). Blue arrows are printed representing protein features. Their direction depicts the strand of the protein (- or +). As RNA features (tRNAs, rRNAs, or other genomic features like binding sites) have no reading frames, they can be found in the middle line of the image, represented by little blue boxes. Hovering over a feature will show a tooltip containing information about the feature, including the name, the position in the genome, the [[Glossary#Functional_role|functional role]] and the [[Glossary#Subsystem|subsystem] it's in. [[Image:GenomeBrowser6fw.png]] === The Control TabView === [[Image:GenomeBrowserLoc.png]] [[Image:GenomeBrowserFeat.png]] 1dabb726bdf35bd2cbd2695f3b765dcbc919f760 1955 1954 2008-11-21T09:45:13Z DanielaBartels 10 /* Genome Browser */ wikitext text/x-wiki == Genome Browser == The Genome Browser enables you to view the features of a genome in their genomic context. The page is divided into three parts, a Control [[WebComponents/Tabview|TabView]], the Six Frame View, and a [[WebComponents/Table|table]] showing all features of an organism. === The Six Frame View === The six frame view represents the six reading frames for proteins (-3, -2, -1, 1, 2, 3). Blue arrows are printed representing protein features. Their direction depicts the strand of the protein (- or +). As RNA features (tRNAs, rRNAs, or other genomic features like binding sites) have no reading frames, they can be found in the middle line of the image, represented by little blue boxes. Hovering over a feature will show a tooltip containing information about the feature, including the name, the position in the genome, the [[Glossary#Functional_role|functional role]] and the [[Glossary#Subsystem|subsystem(s)]] it's in. [[Image:GenomeBrowser6fw.png]] === The Control TabView === [[Image:GenomeBrowserLoc.png]] [[Image:GenomeBrowserFeat.png]] fcef1f389a7eac6874c215a058cec0fed03437ad 1956 1955 2008-11-21T09:54:23Z DanielaBartels 10 /* Genome Browser */ wikitext text/x-wiki == Genome Browser == The Genome Browser enables you to view the features of a genome in their genomic context. The page is divided into three parts, a Control [[WebComponents/Tabview|TabView]], the Six Frame View, and a [[WebComponents/Table|table]] showing all features of an organism. === The Six Frame View === The six frame view represents the six reading frames for proteins (-3, -2, -1, 1, 2, 3). Blue arrows are printed representing protein features. Their direction depicts the strand of the protein (- or +). As RNA features (tRNAs, rRNAs, or other genomic features like binding sites) have no reading frames, they can be found in the middle line of the image, represented by little blue boxes. Hovering over a feature will show a tooltip containing information about the feature, including the name, the position in the genome, the [[Glossary#Functional_role|functional role]] and the [[Glossary#Subsystem|subsystem(s)]] it's in. [[Image:GenomeBrowser6fw.png]] === The Control TabView === Controlling the Six Frame View can be done using the first tab of the Control TabView. You can choose a location the of the genome you want to view by selecting a contig in the '''contig''' drop down menu and stating a '''start position''' on that contig. The zoom of the window can be changed using the '''window''' drop down box. In addition, features can be colored by different metaphors: by subsystem, by filter options of the Feature Table (the features that are present in the table after filtering it will be colored) or by a user defined list you can specify in the '''Upload List''' tab. [[Image:GenomeBrowserLoc.png]] [[Image:GenomeBrowserFeat.png]] 3089a14ec71f8b9cbadfa350fe5a1028f90ff539 1957 1956 2008-11-21T10:07:15Z DanielaBartels 10 /* The Control TabView */ wikitext text/x-wiki == Genome Browser == The Genome Browser enables you to view the features of a genome in their genomic context. The page is divided into three parts, a Control [[WebComponents/Tabview|TabView]], the Six Frame View, and a [[WebComponents/Table|table]] showing all features of an organism. === The Six Frame View === The six frame view represents the six reading frames for proteins (-3, -2, -1, 1, 2, 3). Blue arrows are printed representing protein features. Their direction depicts the strand of the protein (- or +). As RNA features (tRNAs, rRNAs, or other genomic features like binding sites) have no reading frames, they can be found in the middle line of the image, represented by little blue boxes. Hovering over a feature will show a tooltip containing information about the feature, including the name, the position in the genome, the [[Glossary#Functional_role|functional role]] and the [[Glossary#Subsystem|subsystem(s)]] it's in. [[Image:GenomeBrowser6fw.png]] === The Control TabView === Controlling the Six Frame View can be done using the first tab (Location) of the Control TabView. You can choose a location the of the genome you want to view by selecting a contig in the '''contig''' drop down menu and stating a '''start position''' on that contig. The zoom of the window can be changed using the '''window''' drop down box. In addition, features can be colored by different metaphors: by subsystem, by filter options of the Feature Table (the features that are present in the table after filtering it will be colored) or by a user defined list you can specify in the '''Upload List''' tab. Click the button '''Draw''' after making your selections. The arrows '''<=''' and '''=>''' will shift the window over the contig sequence. [[Image:GenomeBrowserLoc.png]] [[Image:GenomeBrowserFeat.png]] 8d73f025d0cff9db0942ee2eab3952bfe167d7ca 1958 1957 2008-11-21T10:09:08Z DanielaBartels 10 /* Genome Browser */ wikitext text/x-wiki == Genome Browser == The Genome Browser enables you to view the features of a genome in their genomic context. The page is divided into three parts, a Control [[WebComponents/Tabview|TabView]], the Six Frame View, and a [[WebComponents/Table|table]] showing all features of an organism. === The Six Frame View === The six frame view represents the six reading frames for proteins (-3, -2, -1, 1, 2, 3). Blue arrows are printed representing protein features. Their direction depicts the strand of the protein (- or +). As RNA features (tRNAs, rRNAs, or other genomic features like binding sites) have no reading frames, they can be found in the middle line of the image, represented by little blue boxes. Hovering over a feature will show a tooltip containing information about the feature, including the name, the position in the genome, the [[Glossary#Functional_role|functional role]] and the [[Glossary#Subsystem|subsystem(s)]] it's in. [[Image:GenomeBrowser6fw.png]] === The Control TabView === Controlling the Six Frame View can be done using the first tab ('''Location''') of the Control TabView. You can choose a location the of the genome you want to view by selecting a contig in the '''contig''' drop down menu and stating a '''start position''' on that contig. The zoom of the window can be changed using the '''window''' drop down box. In addition, features can be colored by different metaphors: by subsystem, by filter options of the Feature Table (the features that are present in the table after filtering it will be colored) or by a user defined list you can specify in the '''Upload List''' tab. Click the button '''Draw''' after making your selections. The arrows '''<=''' and '''=>''' will shift the window over the contig sequence. [[Image:GenomeBrowserLoc.png]] [[Image:GenomeBrowserFeat.png]] 3f550b3c5ec51893aa7f7eaffae434000841d627 1959 1958 2008-11-21T10:12:27Z DanielaBartels 10 /* The Control TabView */ wikitext text/x-wiki == Genome Browser == The Genome Browser enables you to view the features of a genome in their genomic context. The page is divided into three parts, a Control [[WebComponents/Tabview|TabView]], the Six Frame View, and a [[WebComponents/Table|table]] showing all features of an organism. === The Six Frame View === The six frame view represents the six reading frames for proteins (-3, -2, -1, 1, 2, 3). Blue arrows are printed representing protein features. Their direction depicts the strand of the protein (- or +). As RNA features (tRNAs, rRNAs, or other genomic features like binding sites) have no reading frames, they can be found in the middle line of the image, represented by little blue boxes. Hovering over a feature will show a tooltip containing information about the feature, including the name, the position in the genome, the [[Glossary#Functional_role|functional role]] and the [[Glossary#Subsystem|subsystem(s)]] it's in. [[Image:GenomeBrowser6fw.png]] === The Control TabView === Controlling the Six Frame View can be done using the first tab ('''Location''') of the Control TabView. You can choose a location the of the genome you want to view by selecting a contig in the '''contig''' drop down menu and stating a '''start position''' on that contig. The zoom of the window can be changed using the '''window''' drop down box. In addition, features can be colored by different metaphors: by subsystem, by filter options of the Feature Table (the features that are present in the table after filtering it will be colored) or by a user defined list you can specify in the '''Upload List''' tab. Click the button '''Draw''' after making your selections. The arrows '''<=''' and '''=>''' will shift the window over the contig sequence. [[Image:GenomeBrowserLoc.png]] === The Feature Table === [[Image:GenomeBrowserFeat.png]] 70c15b6d6bea4be36bcb8952f0b7012bcd06604b 1960 1959 2008-11-21T10:18:45Z DanielaBartels 10 /* The Control TabView */ wikitext text/x-wiki == Genome Browser == The Genome Browser enables you to view the features of a genome in their genomic context. The page is divided into three parts, a Control [[WebComponents/Tabview|TabView]], the Six Frame View, and a [[WebComponents/Table|table]] showing all features of an organism. === The Six Frame View === The six frame view represents the six reading frames for proteins (-3, -2, -1, 1, 2, 3). Blue arrows are printed representing protein features. Their direction depicts the strand of the protein (- or +). As RNA features (tRNAs, rRNAs, or other genomic features like binding sites) have no reading frames, they can be found in the middle line of the image, represented by little blue boxes. Hovering over a feature will show a tooltip containing information about the feature, including the name, the position in the genome, the [[Glossary#Functional_role|functional role]] and the [[Glossary#Subsystem|subsystem(s)]] it's in. [[Image:GenomeBrowser6fw.png]] === The Control TabView === Controlling the Six Frame View can be done using the first tab ('''Location''') of the Control TabView. You can choose a location the of the genome you want to view by selecting a contig in the '''contig''' drop down menu and stating a '''start position''' on that contig. The zoom of the window can be changed using the '''window''' drop down box. In addition, features can be colored by different metaphors: by subsystem, by filter options of the Feature Table (the features that are present in the table after filtering it will be colored) or by a user defined list you can specify in the '''Upload List''' tab. Click the button '''Draw''' after making your selections. The arrows '''<=''' and '''=>''' will shift the window over the contig sequence. If you have selected a feature in the Six Frame View, the second tab ('''Focus''') will show you information about the feature (the same information you can find in the tooltip by hovering over the feature). Additionally, you will get three buttons that lead to pages that show more detailed information of the selected sequence. [[Image:GenomeBrowserLoc.png]] === The Feature Table === [[Image:GenomeBrowserFeat.png]] 1acaa2d83839526dc4796b1be0025879eceb4dcf 1961 1960 2008-11-21T10:22:37Z DanielaBartels 10 /* The Control TabView */ wikitext text/x-wiki == Genome Browser == The Genome Browser enables you to view the features of a genome in their genomic context. The page is divided into three parts, a Control [[WebComponents/Tabview|TabView]], the Six Frame View, and a [[WebComponents/Table|table]] showing all features of an organism. === The Six Frame View === The six frame view represents the six reading frames for proteins (-3, -2, -1, 1, 2, 3). Blue arrows are printed representing protein features. Their direction depicts the strand of the protein (- or +). As RNA features (tRNAs, rRNAs, or other genomic features like binding sites) have no reading frames, they can be found in the middle line of the image, represented by little blue boxes. Hovering over a feature will show a tooltip containing information about the feature, including the name, the position in the genome, the [[Glossary#Functional_role|functional role]] and the [[Glossary#Subsystem|subsystem(s)]] it's in. [[Image:GenomeBrowser6fw.png]] === The Control TabView === Controlling the Six Frame View can be done using the first tab ('''Location''') of the Control TabView. You can choose a location the of the genome you want to view by selecting a contig in the '''contig''' drop down menu and stating a '''start position''' on that contig. The zoom of the window can be changed using the '''window''' drop down box. In addition, features can be colored by different metaphors: by subsystem, by filter options of the Feature Table (the features that are present in the table after filtering it will be colored) or by a user defined list you can specify in the '''Upload List''' tab. Click the button '''Draw''' after making your selections. The arrows '''<=''' and '''=>''' will shift the window over the contig sequence. If you have selected a feature in the Six Frame View, the second tab ('''Focus''') will show you information about the feature (the same information you can find in the tooltip by hovering over the feature). Additionally, you will get three buttons that lead to pages that show more detailed information about the selected feature. The button '''zoom to sequence''' will show you the '''[[SEED_Viewer_Manual/ContigView|DNA to Protein]] page depicting a detailed sequence view including the DNA sequence, a six frame view of the translation to protein and other features of the sequence in the area of the selected feature. [[Image:GenomeBrowserLoc.png]] === The Feature Table === [[Image:GenomeBrowserFeat.png]] 656a4ee1a59565c66c6eae459437f4e8fb862a1e 1962 1961 2008-11-21T10:30:08Z DanielaBartels 10 /* The Control TabView */ wikitext text/x-wiki == Genome Browser == The Genome Browser enables you to view the features of a genome in their genomic context. The page is divided into three parts, a Control [[WebComponents/Tabview|TabView]], the Six Frame View, and a [[WebComponents/Table|table]] showing all features of an organism. === The Six Frame View === The six frame view represents the six reading frames for proteins (-3, -2, -1, 1, 2, 3). Blue arrows are printed representing protein features. Their direction depicts the strand of the protein (- or +). As RNA features (tRNAs, rRNAs, or other genomic features like binding sites) have no reading frames, they can be found in the middle line of the image, represented by little blue boxes. Hovering over a feature will show a tooltip containing information about the feature, including the name, the position in the genome, the [[Glossary#Functional_role|functional role]] and the [[Glossary#Subsystem|subsystem(s)]] it's in. [[Image:GenomeBrowser6fw.png]] === The Control TabView === Controlling the Six Frame View can be done using the first tab ('''Location''') of the Control TabView. You can choose a location the of the genome you want to view by selecting a contig in the '''contig''' drop down menu and stating a '''start position''' on that contig. The zoom of the window can be changed using the '''window''' drop down box. In addition, features can be colored by different metaphors: by subsystem, by filter options of the Feature Table (the features that are present in the table after filtering it will be colored) or by a user defined list you can specify in the '''Upload List''' tab. Click the button '''Draw''' after making your selections. The arrows '''<=''' and '''=>''' will shift the window over the contig sequence. If you have selected a feature in the Six Frame View, the second tab ('''Focus''') will show you information about the feature (the same information you can find in the tooltip by hovering over the feature). Additionally, you will get three buttons that lead to pages that show more detailed information about the selected feature. The button '''zoom to sequence''' will show you the '''[[SEED_Viewer_Manual/ContigView|DNA to Protein]]''' page depicting a detailed sequence view including the DNA sequence, a six frame view of the translation to protein and other features of the sequence in the area of the selected feature. Clicking '''details page''' leads to the [[SEED_Viewer_Manual/Annotation|Annotation]] page of the feature. You will see all known details about the feature, as well as the [[SEED_Viewer_Manual/Annotation#CompareRegions|Compare regions view]] centered on the feature. The '''evidence''' button leads to the [[SEED_Viewer_Manual/Evidence|Evidence]] page showing evidence for the annotation of the feature in form of [[Glossary/Similarities|Similarities]] and protein domains. [[Image:GenomeBrowserLoc.png]] === The Feature Table === [[Image:GenomeBrowserFeat.png]] a7b9b294b79945c8e80cc3b9a89a71041d7c6b63 1963 1962 2008-11-21T10:55:23Z DanielaBartels 10 /* The Control TabView */ wikitext text/x-wiki == Genome Browser == The Genome Browser enables you to view the features of a genome in their genomic context. The page is divided into three parts, a Control [[WebComponents/Tabview|TabView]], the Six Frame View, and a [[WebComponents/Table|table]] showing all features of an organism. === The Six Frame View === The six frame view represents the six reading frames for proteins (-3, -2, -1, 1, 2, 3). Blue arrows are printed representing protein features. Their direction depicts the strand of the protein (- or +). As RNA features (tRNAs, rRNAs, or other genomic features like binding sites) have no reading frames, they can be found in the middle line of the image, represented by little blue boxes. Hovering over a feature will show a tooltip containing information about the feature, including the name, the position in the genome, the [[Glossary#Functional_role|functional role]] and the [[Glossary#Subsystem|subsystem(s)]] it's in. [[Image:GenomeBrowser6fw.png]] === The Control TabView === Controlling the Six Frame View can be done using the first tab ('''Location''') of the Control TabView. You can choose a location the of the genome you want to view by selecting a contig in the '''contig''' drop down menu and stating a '''start position''' on that contig. The zoom of the window can be changed using the '''window''' drop down box. In addition, features can be colored by different metaphors: by subsystem, by filter options of the Feature Table (the features that are present in the table after filtering it will be colored) or by a user defined list you can specify in the '''Upload List''' tab. Click the button '''Draw''' after making your selections. The arrows '''<=''' and '''=>''' will shift the window over the contig sequence. If you have selected a feature in the Six Frame View, the second tab ('''Focus''') will show you information about the feature (the same information you can find in the tooltip by hovering over the feature). Additionally, you will get three buttons that lead to pages that show more detailed information about the selected feature. The button '''zoom to sequence''' will show you the '''[[SEED_Viewer_Manual/ContigView|DNA to Protein]]''' page depicting a detailed sequence view including the DNA sequence, a six frame view of the translation to protein and other features of the sequence in the area of the selected feature. Clicking '''details page''' leads to the [[SEED_Viewer_Manual/Annotation|Annotation]] page of the feature. You will see all known details about the feature, as well as the [[SEED_Viewer_Manual/Annotation#CompareRegions|Compare regions view]] centered on the feature. The '''evidence''' button leads to the [[SEED_Viewer_Manual/Evidence|Evidence]] page showing evidence for the annotation of the feature in form of [[Glossary/Similarities|Similarities]] and protein domains. '''Upload a list''' - will let you upload a list of locations of BLAST hits of the form (Contig, Start, Stop, ID). The list has to be in plain text format, meaning not an Excel table. If you have an Excel table containing the information, save the list as '''text (tab delimited)''' in Excel. If you have successfully uploaded a list, you will now be able to navigate the regions in your list. They are shown on the middle line in the Six Frame View in form of little boxes. [[Image:GenomeBrowserLoc.png]] === The Feature Table === [[Image:GenomeBrowserFeat.png]] d8a77927b1be7c1f1ff2320170cf2bfdb4a71920 1964 1963 2008-11-21T10:59:17Z DanielaBartels 10 /* The Feature Table */ wikitext text/x-wiki == Genome Browser == The Genome Browser enables you to view the features of a genome in their genomic context. The page is divided into three parts, a Control [[WebComponents/Tabview|TabView]], the Six Frame View, and a [[WebComponents/Table|table]] showing all features of an organism. === The Six Frame View === The six frame view represents the six reading frames for proteins (-3, -2, -1, 1, 2, 3). Blue arrows are printed representing protein features. Their direction depicts the strand of the protein (- or +). As RNA features (tRNAs, rRNAs, or other genomic features like binding sites) have no reading frames, they can be found in the middle line of the image, represented by little blue boxes. Hovering over a feature will show a tooltip containing information about the feature, including the name, the position in the genome, the [[Glossary#Functional_role|functional role]] and the [[Glossary#Subsystem|subsystem(s)]] it's in. [[Image:GenomeBrowser6fw.png]] === The Control TabView === Controlling the Six Frame View can be done using the first tab ('''Location''') of the Control TabView. You can choose a location the of the genome you want to view by selecting a contig in the '''contig''' drop down menu and stating a '''start position''' on that contig. The zoom of the window can be changed using the '''window''' drop down box. In addition, features can be colored by different metaphors: by subsystem, by filter options of the Feature Table (the features that are present in the table after filtering it will be colored) or by a user defined list you can specify in the '''Upload List''' tab. Click the button '''Draw''' after making your selections. The arrows '''<=''' and '''=>''' will shift the window over the contig sequence. If you have selected a feature in the Six Frame View, the second tab ('''Focus''') will show you information about the feature (the same information you can find in the tooltip by hovering over the feature). Additionally, you will get three buttons that lead to pages that show more detailed information about the selected feature. The button '''zoom to sequence''' will show you the '''[[SEED_Viewer_Manual/ContigView|DNA to Protein]]''' page depicting a detailed sequence view including the DNA sequence, a six frame view of the translation to protein and other features of the sequence in the area of the selected feature. Clicking '''details page''' leads to the [[SEED_Viewer_Manual/Annotation|Annotation]] page of the feature. You will see all known details about the feature, as well as the [[SEED_Viewer_Manual/Annotation#CompareRegions|Compare regions view]] centered on the feature. The '''evidence''' button leads to the [[SEED_Viewer_Manual/Evidence|Evidence]] page showing evidence for the annotation of the feature in form of [[Glossary/Similarities|Similarities]] and protein domains. '''Upload a list''' - will let you upload a list of locations of BLAST hits of the form (Contig, Start, Stop, ID). The list has to be in plain text format, meaning not an Excel table. If you have an Excel table containing the information, save the list as '''text (tab delimited)''' in Excel. If you have successfully uploaded a list, you will now be able to navigate the regions in your list. They are shown on the middle line in the Six Frame View in form of little boxes. [[Image:GenomeBrowserLoc.png]] === The Feature Table === The Feature Table shows all features present in your organism in a [[WebComponents/Table|table]]. Information you can see for a feature are its ID, Type (e.g. CDS, RNA and others), its locations (Contig, Start, Stop) and length as well as the functional role it's annotated with and the subsystems it belongs to. The button in the last column (Region) will center the Six Frame View on this feature and select it. [[Image:GenomeBrowserFeat.png]] d585d2580dee925dc27c81ba9a7ff3f33b7d39c3 1965 1964 2008-11-21T11:01:04Z TobiasPaczian 17 /* The Six Frame View */ wikitext text/x-wiki == Genome Browser == The Genome Browser enables you to view the features of a genome in their genomic context. The page is divided into three parts, a Control [[WebComponents/Tabview|TabView]], the Six Frame View, and a [[WebComponents/Table|table]] showing all features of an organism. === The Six Frame View === The six frame view represents the six reading frames for proteins (-3, -2, -1, 1, 2, 3). Blue arrows are printed representing protein features. Their direction depicts the strand of the protein (- or +). As RNA features (tRNAs, rRNAs, or other genomic features like binding sites) have no reading frames. They can be found in the middle line of the image, represented by little blue boxes. Hovering over a feature will show a tooltip containing information about the feature, including the name, the position in the genome, the [[Glossary#Functional_role|functional role]] and the [[Glossary#Subsystem|subsystem(s)]] it's in. [[Image:GenomeBrowser6fw.png]] === The Control TabView === Controlling the Six Frame View can be done using the first tab ('''Location''') of the Control TabView. You can choose a location the of the genome you want to view by selecting a contig in the '''contig''' drop down menu and stating a '''start position''' on that contig. The zoom of the window can be changed using the '''window''' drop down box. In addition, features can be colored by different metaphors: by subsystem, by filter options of the Feature Table (the features that are present in the table after filtering it will be colored) or by a user defined list you can specify in the '''Upload List''' tab. Click the button '''Draw''' after making your selections. The arrows '''<=''' and '''=>''' will shift the window over the contig sequence. If you have selected a feature in the Six Frame View, the second tab ('''Focus''') will show you information about the feature (the same information you can find in the tooltip by hovering over the feature). Additionally, you will get three buttons that lead to pages that show more detailed information about the selected feature. The button '''zoom to sequence''' will show you the '''[[SEED_Viewer_Manual/ContigView|DNA to Protein]]''' page depicting a detailed sequence view including the DNA sequence, a six frame view of the translation to protein and other features of the sequence in the area of the selected feature. Clicking '''details page''' leads to the [[SEED_Viewer_Manual/Annotation|Annotation]] page of the feature. You will see all known details about the feature, as well as the [[SEED_Viewer_Manual/Annotation#CompareRegions|Compare regions view]] centered on the feature. The '''evidence''' button leads to the [[SEED_Viewer_Manual/Evidence|Evidence]] page showing evidence for the annotation of the feature in form of [[Glossary/Similarities|Similarities]] and protein domains. '''Upload a list''' - will let you upload a list of locations of BLAST hits of the form (Contig, Start, Stop, ID). The list has to be in plain text format, meaning not an Excel table. If you have an Excel table containing the information, save the list as '''text (tab delimited)''' in Excel. If you have successfully uploaded a list, you will now be able to navigate the regions in your list. They are shown on the middle line in the Six Frame View in form of little boxes. [[Image:GenomeBrowserLoc.png]] === The Feature Table === The Feature Table shows all features present in your organism in a [[WebComponents/Table|table]]. Information you can see for a feature are its ID, Type (e.g. CDS, RNA and others), its locations (Contig, Start, Stop) and length as well as the functional role it's annotated with and the subsystems it belongs to. The button in the last column (Region) will center the Six Frame View on this feature and select it. [[Image:GenomeBrowserFeat.png]] 161da9db4c0829c5fd84c4ca28ae387a5b7c1d7c 6 1490 1944 2008-11-18T16:47:01Z DanielaBartels 10 wikitext text/x-wiki da39a3ee5e6b4b0d3255bfef95601890afd80709 6 1491 1948 2008-11-18T16:52:28Z DanielaBartels 10 wikitext text/x-wiki da39a3ee5e6b4b0d3255bfef95601890afd80709 6 1492 1950 2008-11-18T17:01:45Z DanielaBartels 10 wikitext text/x-wiki da39a3ee5e6b4b0d3255bfef95601890afd80709 0 1493 1966 2008-11-21T11:45:24Z DanielaBartels 10 wikitext text/x-wiki == Annotation == The Annotation page shows a lot of information about a single feature like a protein or an RNA. [[Image:AnnotationFeat.png]] 93c82c9176f91b3503962ac9778a8989648e5f31 1968 1966 2008-11-21T11:49:19Z DanielaBartels 10 /* Annotation */ wikitext text/x-wiki == Annotation == The Annotation page shows a variaty of information about a single feature like a protein or an RNA. [[Image:AnnotationFeat.png]] 977bd341f6487bb5ce889453fc98d3bdd185642a 1969 1968 2008-11-21T11:55:59Z DanielaBartels 10 /* Annotation */ wikitext text/x-wiki == Annotation == The Annotation page shows a variaty of information about a single feature like a protein or an RNA. The page is roughly divided into three parts. The '''Annotation Overview''' presents the basic information about the feature. '''Reasons for Current Assignment''' reflect why the feature was assigned with the current functional role. The third part is a Compare Regions View showing the region of the feature in context to its own and related genomes. === The Annotation Overview === [[Image:AnnotationFeat.png]] b1d39de615fbba9e3c1dcbae59f1f2c1a5e697b0 1970 1969 2008-11-21T11:56:15Z DanielaBartels 10 /* Annotation */ wikitext text/x-wiki == Annotation == The Annotation page shows a variaty of information about a single feature like a protein or an RNA. The page is roughly divided into three parts. The '''Annotation Overview''' presents the basic information about the feature. '''Reasons for Current Assignment''' reflect why the feature was assigned with the current functional role. The third part is a '''Compare Regions View''' showing the region of the feature in context to its own and related genomes. === The Annotation Overview === [[Image:AnnotationFeat.png]] 8aef74b87cd58aafff965dbc5d7f260e959812fa 1973 1970 2008-11-21T11:58:50Z DanielaBartels 10 /* Annotation */ wikitext text/x-wiki == Annotation == The Annotation page shows a variaty of information about a single feature like a protein or an RNA. The page is roughly divided into three parts. The '''Annotation Overview''' presents the basic information about the feature. '''Reasons for Current Assignment''' reflect why the feature was assigned with the current functional role. The third part is a '''Compare Regions View''' showing the region of the feature in context to its own and related genomes. === The Annotation Overview === [[Image:AnnotationFeat.png]] === Reasons for Current Assignment === === Compare Regions === 3515b8053023b696b56d3420de77ff2512a68e34 1974 1973 2008-11-21T12:01:50Z DanielaBartels 10 /* Annotation */ wikitext text/x-wiki == Annotation == The Annotation page shows a variaty of information about a single feature like a protein or an RNA. The page is roughly divided into three parts. The '''Annotation Overview''' presents the basic information about the feature. '''Reasons for Current Assignment''' reflect why the feature was assigned with the current functional role. The third part is a '''Compare Regions View''' showing the region of the feature in context to its own and related genomes. === The Annotation Overview === [[Image:AnnotationFeat.png]] === Reasons for Current Assignment === [[Image:AnnotationAnno.png]] === Compare Regions === [[Image:AnnotationComp.png]] bdbd4ddb46d8678f8b69be86f630a04d56cb0b31 6 1494 1967 2008-11-21T11:45:55Z DanielaBartels 10 wikitext text/x-wiki da39a3ee5e6b4b0d3255bfef95601890afd80709 6 1495 1975 2008-11-21T12:02:04Z DanielaBartels 10 wikitext text/x-wiki da39a3ee5e6b4b0d3255bfef95601890afd80709 6 1496 1976 2008-11-21T12:02:22Z DanielaBartels 10 wikitext text/x-wiki da39a3ee5e6b4b0d3255bfef95601890afd80709 6 1497 1977 2008-11-21T12:03:51Z DanielaBartels 10 wikitext text/x-wiki da39a3ee5e6b4b0d3255bfef95601890afd80709 0 1493 1978 1974 2008-11-21T12:04:44Z DanielaBartels 10 /* Reasons for Current Assignment */ wikitext text/x-wiki == Annotation == The Annotation page shows a variaty of information about a single feature like a protein or an RNA. The page is roughly divided into three parts. The '''Annotation Overview''' presents the basic information about the feature. '''Reasons for Current Assignment''' reflect why the feature was assigned with the current functional role. The third part is a '''Compare Regions View''' showing the region of the feature in context to its own and related genomes. === The Annotation Overview === [[Image:AnnotationFeat.png]] === Reasons for Current Assignment === [[Image:AnnotationAnnot.png]] === Compare Regions === [[Image:AnnotationComp.png]] d50a4e9153f2920371e60cc20fbb7607fc7b5f46 1979 1978 2008-11-21T12:07:54Z DanielaBartels 10 /* Annotation */ wikitext text/x-wiki == Annotation == The Annotation page shows a variaty of information about a single feature like a protein or an RNA. The page is roughly divided into three parts. The '''Annotation Overview''' presents the basic information about the feature. '''Reasons for Current Assignment''' reflect why the feature was assigned with the current functional role. The third part is a '''Compare Regions View''' showing the region of the feature in context to its own and related genomes. If you are logged in and the feature belongs to your private genome, this page will have additional options for you to annotate the feature. These are described [[SEED_Viewer_Manual/Editing_Capabilities/Annotation|here]] === The Annotation Overview === [[Image:AnnotationFeat.png]] === Reasons for Current Assignment === [[Image:AnnotationAnnot.png]] === Compare Regions === [[Image:AnnotationComp.png]] 9d2d0ef344e23ed4ae8fd7ce34fefa864d0ef8a9 1980 1979 2008-11-21T12:11:10Z DanielaBartels 10 /* Annotation */ wikitext text/x-wiki == Annotation == The Annotation page shows a variaty of information about a single feature like a protein or an RNA. The page is roughly divided into three parts. The '''Annotation Overview''' presents the basic information about the feature. '''Reasons for Current Assignment''' reflect why the feature was assigned with the current functional role. The third part is a '''Compare Regions View''' showing the region of the feature in context to its own and related genomes. If you are logged in and the feature belongs to your private genome, this page will have additional options for you to annotate the feature. These are described [[SEED_Viewer_Manual/Editing_Capabilities/Annotation|here]]. === The Annotation Overview === The feature ID and the genome it belongs to are shown in the header line of this part of the page. They link to [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] and the [[SEED_Viewer_Manual/Organism|Organism Page]], respectively. [[Image:AnnotationFeat.png]] === Reasons for Current Assignment === [[Image:AnnotationAnnot.png]] === Compare Regions === [[Image:AnnotationComp.png]] 9f14bd52b32dfb22b5451baf0f88c50fad65db1d 1981 1980 2008-11-21T12:11:43Z DanielaBartels 10 /* The Annotation Overview */ wikitext text/x-wiki == Annotation == The Annotation page shows a variaty of information about a single feature like a protein or an RNA. The page is roughly divided into three parts. The '''Annotation Overview''' presents the basic information about the feature. '''Reasons for Current Assignment''' reflect why the feature was assigned with the current functional role. The third part is a '''Compare Regions View''' showing the region of the feature in context to its own and related genomes. If you are logged in and the feature belongs to your private genome, this page will have additional options for you to annotate the feature. These are described [[SEED_Viewer_Manual/Editing_Capabilities/Annotation|here]]. === The Annotation Overview === The feature ID and the genome it belongs to are shown in the header line of this part of the page. They link to [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] and the [[SEED_Viewer_Manual/OrganismPage|Organism Page]], respectively. [[Image:AnnotationFeat.png]] === Reasons for Current Assignment === [[Image:AnnotationAnnot.png]] === Compare Regions === [[Image:AnnotationComp.png]] f43b4f8a470856ed98ec7904bac60aa1939336ff 1982 1981 2008-11-21T12:14:59Z DanielaBartels 10 /* The Annotation Overview */ wikitext text/x-wiki == Annotation == The Annotation page shows a variaty of information about a single feature like a protein or an RNA. The page is roughly divided into three parts. The '''Annotation Overview''' presents the basic information about the feature. '''Reasons for Current Assignment''' reflect why the feature was assigned with the current functional role. The third part is a '''Compare Regions View''' showing the region of the feature in context to its own and related genomes. If you are logged in and the feature belongs to your private genome, this page will have additional options for you to annotate the feature. These are described [[SEED_Viewer_Manual/Editing_Capabilities/Annotation|here]]. === The Annotation Overview === The feature ID and the genome it belongs to are shown in the header line of this part of the page. They link to [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] and the [[SEED_Viewer_Manual/OrganismPage|Organism Page]], respectively. The '''current annotation''' depicts the functional role that is currently assigned to the feature. As annotations can be changed by users, you have the option to view an annotation history by pressing the '''show''' button in the cell '''annotation history''' some rows below. It will open a small table listing the date, the curator and the annotation that was made for each entry. [[Image:AnnotationFeat.png]] === Reasons for Current Assignment === [[Image:AnnotationAnnot.png]] === Compare Regions === [[Image:AnnotationComp.png]] adf60ae18549435b111079030b95b2d7c02ebcdb 1983 1982 2008-11-21T12:18:37Z DanielaBartels 10 /* The Annotation Overview */ wikitext text/x-wiki == Annotation == The Annotation page shows a variaty of information about a single feature like a protein or an RNA. The page is roughly divided into three parts. The '''Annotation Overview''' presents the basic information about the feature. '''Reasons for Current Assignment''' reflect why the feature was assigned with the current functional role. The third part is a '''Compare Regions View''' showing the region of the feature in context to its own and related genomes. If you are logged in and the feature belongs to your private genome, this page will have additional options for you to annotate the feature. These are described [[SEED_Viewer_Manual/Editing_Capabilities/Annotation|here]]. === The Annotation Overview === The feature ID and the genome it belongs to are shown in the header line of this part of the page. They link to [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] and the [[SEED_Viewer_Manual/OrganismPage|Organism Page]], respectively. The '''current annotation''' depicts the functional role that is currently assigned to the feature. As annotations can be changed by users, you have the option to view an annotation history by pressing the '''show''' button in the cell '''annotation history''' some rows below. It will open a small table listing the date, the curator and the annotation that was made for each entry. As the genome name for the feature is already presented in the header of this section, we additionally show the '''taxonomy id''' for that genome in the overview. The link will lead to the Taxonomy Browser at the NCBI showing the taxonomy information for that genome. [[Image:AnnotationFeat.png]] === Reasons for Current Assignment === [[Image:AnnotationAnnot.png]] === Compare Regions === [[Image:AnnotationComp.png]] 79d61fc1da048bf923a587ddd104eb8e5641fc16 1984 1983 2008-11-21T12:26:07Z DanielaBartels 10 /* The Annotation Overview */ wikitext text/x-wiki == Annotation == The Annotation page shows a variaty of information about a single feature like a protein or an RNA. The page is roughly divided into three parts. The '''Annotation Overview''' presents the basic information about the feature. '''Reasons for Current Assignment''' reflect why the feature was assigned with the current functional role. The third part is a '''Compare Regions View''' showing the region of the feature in context to its own and related genomes. If you are logged in and the feature belongs to your private genome, this page will have additional options for you to annotate the feature. These are described [[SEED_Viewer_Manual/Editing_Capabilities/Annotation|here]]. === The Annotation Overview === The feature ID and the genome it belongs to are shown in the header line of this part of the page. They link to [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] and the [[SEED_Viewer_Manual/OrganismPage|Organism Page]], respectively. The '''current annotation''' depicts the functional role that is currently assigned to the feature. As annotations can be changed by users, you have the option to view an annotation history by pressing the '''show''' button in the cell '''annotation history''' some rows below. It will open a small table listing the date, the curator and the annotation that was made for each entry. As the genome name for the feature is already presented in the header of this section, we additionally show the '''taxonomy id''' for that genome in the overview. The link will lead to the Taxonomy Browser at the NCBI showing the taxonomy information for that genome. The '''internal links''' you can see in the next row are leading to different pages containing other views and information for the feature. The [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] ('''genome browser''') displays the feature in the context of its genome. '''evidence''' leads to the [[SEED_Viewer_Manual/Evidence|Evidence]] page showing evidence for the annotation of the feature in form of [[Glossary/Similarities|Similarities]] and protein domains. Downloading the actual sequence for the feature is possible using the [[SEED_Viewer_Manual/ShowSeqs|Sequence Page]] ('''sequence''') link. [[Image:AnnotationFeat.png]] === Reasons for Current Assignment === [[Image:AnnotationAnnot.png]] === Compare Regions === [[Image:AnnotationComp.png]] 30cf9a53413749c74b8c163357be8f802b66b027 1985 1984 2008-11-21T14:04:07Z DanielaBartels 10 /* The Annotation Overview */ wikitext text/x-wiki == Annotation == The Annotation page shows a variaty of information about a single feature like a protein or an RNA. The page is roughly divided into three parts. The '''Annotation Overview''' presents the basic information about the feature. '''Reasons for Current Assignment''' reflect why the feature was assigned with the current functional role. The third part is a '''Compare Regions View''' showing the region of the feature in context to its own and related genomes. If you are logged in and the feature belongs to your private genome, this page will have additional options for you to annotate the feature. These are described [[SEED_Viewer_Manual/Editing_Capabilities/Annotation|here]]. === The Annotation Overview === The feature ID and the genome it belongs to are shown in the header line of this part of the page. They link to [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] and the [[SEED_Viewer_Manual/OrganismPage|Organism Page]], respectively. The '''current annotation''' depicts the functional role that is currently assigned to the feature. As annotations can be changed by users, you have the option to view an annotation history by pressing the '''show''' button in the cell '''annotation history''' some rows below. It will open a small table listing the date, the curator and the annotation that was made for each entry. As the genome name for the feature is already presented in the header of this section, we additionally show the '''taxonomy id''' for that genome in the overview. The link will lead to the Taxonomy Browser at the NCBI showing the taxonomy information for that genome. The '''internal links''' you can see in the next row are leading to different pages containing other views and information for the feature. The [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] ('''genome browser''') displays the feature in the context of its genome. '''evidence''' leads to the [[SEED_Viewer_Manual/Evidence|Evidence]] page showing evidence for the annotation of the feature in form of [[Glossary/Similarities|Similarities]] and protein domains. Downloading the actual sequence for the feature is possible using the [[SEED_Viewer_Manual/ShowSeqs|Sequence Page]] ('''sequence''') link. At '''PubMed Links''' you can see the PubMed IDs to papers linked to the NCBI Entrez Database. The PubMed IDs shown are direct literature links attached directly to a feature, so-called '''dlits'''. '''FIGfams''' are protein families based on the subsystems technology. If you find an entry in this fields, the feature is part of the stated FIGfam. The link leads to the [[SEED_Viewer_Manual/FIGfams|FIGfam Viewer]]. [[Image:AnnotationFeat.png]] === Reasons for Current Assignment === [[Image:AnnotationAnnot.png]] === Compare Regions === [[Image:AnnotationComp.png]] 012b4d98e4449d5142eee05561aab90a7ea8ce77 1986 1985 2008-11-21T14:06:56Z DanielaBartels 10 /* The Annotation Overview */ wikitext text/x-wiki == Annotation == The Annotation page shows a variaty of information about a single feature like a protein or an RNA. The page is roughly divided into three parts. The '''Annotation Overview''' presents the basic information about the feature. '''Reasons for Current Assignment''' reflect why the feature was assigned with the current functional role. The third part is a '''Compare Regions View''' showing the region of the feature in context to its own and related genomes. If you are logged in and the feature belongs to your private genome, this page will have additional options for you to annotate the feature. These are described [[SEED_Viewer_Manual/Editing_Capabilities/Annotation|here]]. === The Annotation Overview === The feature ID and the genome it belongs to are shown in the header line of this part of the page. They link to [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] and the [[SEED_Viewer_Manual/OrganismPage|Organism Page]], respectively. The '''current annotation''' depicts the functional role that is currently assigned to the feature. As annotations can be changed by users, you have the option to view an annotation history by pressing the '''show''' button in the cell '''annotation history''' some rows below. It will open a small table listing the date, the curator and the annotation that was made for each entry. As the genome name for the feature is already presented in the header of this section, we additionally show the '''taxonomy id''' for that genome in the overview. The link will lead to the Taxonomy Browser at the NCBI showing the taxonomy information for that genome. The '''internal links''' you can see in the next row are leading to different pages containing other views and information for the feature. The [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] ('''genome browser''') displays the feature in the context of its genome. '''evidence''' leads to the [[SEED_Viewer_Manual/Evidence|Evidence]] page showing evidence for the annotation of the feature in form of [[Glossary/Similarities|Similarities]] and protein domains. Downloading the actual sequence for the feature is possible using the [[SEED_Viewer_Manual/ShowSeqs|Sequence Page]] ('''sequence''') link. At '''PubMed Links''' you can see the PubMed IDs to papers linked to the NCBI Entrez Database. The PubMed IDs shown are direct literature links attached directly to a feature, so-called '''dlits'''. '''FIGfams''' are protein families based on the subsystems technology. If you find an entry in this fields, the feature is part of the stated FIGfam. The link leads to the [[SEED_Viewer_Manual/FIGfams|FIGfam Viewer]]. '''database cross references''' link the feature to its entries in other databases like [[www.uniprot.org|UniProt]], [[Image:AnnotationFeat.png]] === Reasons for Current Assignment === [[Image:AnnotationAnnot.png]] === Compare Regions === [[Image:AnnotationComp.png]] cb385e39312f9b55f92c87fd45b4dcda34fc16db 1987 1986 2008-11-21T14:11:36Z DanielaBartels 10 /* The Annotation Overview */ wikitext text/x-wiki == Annotation == The Annotation page shows a variaty of information about a single feature like a protein or an RNA. The page is roughly divided into three parts. The '''Annotation Overview''' presents the basic information about the feature. '''Reasons for Current Assignment''' reflect why the feature was assigned with the current functional role. The third part is a '''Compare Regions View''' showing the region of the feature in context to its own and related genomes. If you are logged in and the feature belongs to your private genome, this page will have additional options for you to annotate the feature. These are described [[SEED_Viewer_Manual/Editing_Capabilities/Annotation|here]]. === The Annotation Overview === The feature ID and the genome it belongs to are shown in the header line of this part of the page. They link to [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] and the [[SEED_Viewer_Manual/OrganismPage|Organism Page]], respectively. The '''current annotation''' depicts the functional role that is currently assigned to the feature. As annotations can be changed by users, you have the option to view an annotation history by pressing the '''show''' button in the cell '''annotation history''' some rows below. It will open a small table listing the date, the curator and the annotation that was made for each entry. As the genome name for the feature is already presented in the header of this section, we additionally show the '''taxonomy id''' for that genome in the overview. The link will lead to the Taxonomy Browser at the NCBI showing the taxonomy information for that genome. The '''internal links''' you can see in the next row are leading to different pages containing other views and information for the feature. The [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] ('''genome browser''') displays the feature in the context of its genome. '''evidence''' leads to the [[SEED_Viewer_Manual/Evidence|Evidence]] page showing evidence for the annotation of the feature in form of [[Glossary/Similarities|Similarities]] and protein domains. Downloading the actual sequence for the feature is possible using the [[SEED_Viewer_Manual/ShowSeqs|Sequence Page]] ('''sequence''') link. At '''PubMed Links''' you can see the PubMed IDs to papers linked to the NCBI Entrez Database. The PubMed IDs shown are direct literature links attached directly to a feature, so-called '''dlits'''. '''FIGfams''' are protein families based on the subsystems technology. If you find an entry in this fields, the feature is part of the stated FIGfam. The link leads to the [[SEED_Viewer_Manual/FIGfams|FIGfam Viewer]]. '''database cross references''' link the feature to its entries in other databases like [www.uniprot.org UniProt], [[Image:AnnotationFeat.png]] === Reasons for Current Assignment === [[Image:AnnotationAnnot.png]] === Compare Regions === [[Image:AnnotationComp.png]] cee761c0d9dfc76fdea9e21688a7a736630a43af 1988 1987 2008-11-21T14:12:33Z DanielaBartels 10 /* The Annotation Overview */ wikitext text/x-wiki == Annotation == The Annotation page shows a variaty of information about a single feature like a protein or an RNA. The page is roughly divided into three parts. The '''Annotation Overview''' presents the basic information about the feature. '''Reasons for Current Assignment''' reflect why the feature was assigned with the current functional role. The third part is a '''Compare Regions View''' showing the region of the feature in context to its own and related genomes. If you are logged in and the feature belongs to your private genome, this page will have additional options for you to annotate the feature. These are described [[SEED_Viewer_Manual/Editing_Capabilities/Annotation|here]]. === The Annotation Overview === The feature ID and the genome it belongs to are shown in the header line of this part of the page. They link to [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] and the [[SEED_Viewer_Manual/OrganismPage|Organism Page]], respectively. The '''current annotation''' depicts the functional role that is currently assigned to the feature. As annotations can be changed by users, you have the option to view an annotation history by pressing the '''show''' button in the cell '''annotation history''' some rows below. It will open a small table listing the date, the curator and the annotation that was made for each entry. As the genome name for the feature is already presented in the header of this section, we additionally show the '''taxonomy id''' for that genome in the overview. The link will lead to the Taxonomy Browser at the NCBI showing the taxonomy information for that genome. The '''internal links''' you can see in the next row are leading to different pages containing other views and information for the feature. The [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] ('''genome browser''') displays the feature in the context of its genome. '''evidence''' leads to the [[SEED_Viewer_Manual/Evidence|Evidence]] page showing evidence for the annotation of the feature in form of [[Glossary/Similarities|Similarities]] and protein domains. Downloading the actual sequence for the feature is possible using the [[SEED_Viewer_Manual/ShowSeqs|Sequence Page]] ('''sequence''') link. At '''PubMed Links''' you can see the PubMed IDs to papers linked to the NCBI Entrez Database. The PubMed IDs shown are direct literature links attached directly to a feature, so-called '''dlits'''. '''FIGfams''' are protein families based on the subsystems technology. If you find an entry in this fields, the feature is part of the stated FIGfam. The link leads to the [[SEED_Viewer_Manual/FIGfams|FIGfam Viewer]]. '''database cross references''' link the feature to its entries in other databases like [[www.uniprot.org UniProt]], [[Image:AnnotationFeat.png]] === Reasons for Current Assignment === [[Image:AnnotationAnnot.png]] === Compare Regions === [[Image:AnnotationComp.png]] 3ec38c70d85e645170109e5c43bcfdf063104f55 1989 1988 2008-11-21T14:19:35Z DanielaBartels 10 /* The Annotation Overview */ wikitext text/x-wiki == Annotation == The Annotation page shows a variaty of information about a single feature like a protein or an RNA. The page is roughly divided into three parts. The '''Annotation Overview''' presents the basic information about the feature. '''Reasons for Current Assignment''' reflect why the feature was assigned with the current functional role. The third part is a '''Compare Regions View''' showing the region of the feature in context to its own and related genomes. If you are logged in and the feature belongs to your private genome, this page will have additional options for you to annotate the feature. These are described [[SEED_Viewer_Manual/Editing_Capabilities/Annotation|here]]. === The Annotation Overview === The feature ID and the genome it belongs to are shown in the header line of this part of the page. They link to [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] and the [[SEED_Viewer_Manual/OrganismPage|Organism Page]], respectively. The '''current annotation''' depicts the functional role that is currently assigned to the feature. As annotations can be changed by users, you have the option to view an annotation history by pressing the '''show''' button in the cell '''annotation history''' some rows below. It will open a small table listing the date, the curator and the annotation that was made for each entry. As the genome name for the feature is already presented in the header of this section, we additionally show the '''taxonomy id''' for that genome in the overview. The link will lead to the Taxonomy Browser at the NCBI showing the taxonomy information for that genome. The '''internal links''' you can see in the next row are leading to different pages containing other views and information for the feature. The [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] ('''genome browser''') displays the feature in the context of its genome. '''evidence''' leads to the [[SEED_Viewer_Manual/Evidence|Evidence]] page showing evidence for the annotation of the feature in form of [[Glossary/Similarities|Similarities]] and protein domains. Downloading the actual sequence for the feature is possible using the [[SEED_Viewer_Manual/ShowSeqs|Sequence Page]] ('''sequence''') link. At '''PubMed Links''' you can see the PubMed IDs to papers linked to the NCBI Entrez Database. The PubMed IDs shown are direct literature links attached directly to a feature, so-called '''dlits'''. '''FIGfams''' are protein families based on the subsystems technology. If you find an entry in this fields, the feature is part of the stated FIGfam. The link leads to the [[SEED_Viewer_Manual/FIGfams|FIGfam Viewer]]. '''database cross references''' link the feature to its entries (Aliases) in other databases like UniProt, GenBANK and many others. [[Image:AnnotationFeat.png]] === Reasons for Current Assignment === [[Image:AnnotationAnnot.png]] === Compare Regions === [[Image:AnnotationComp.png]] 5e3df60620918295463b09fd73c491c3cad0c94f 1990 1989 2008-11-21T14:23:40Z DanielaBartels 10 /* The Annotation Overview */ wikitext text/x-wiki == Annotation == The Annotation page shows a variaty of information about a single feature like a protein or an RNA. The page is roughly divided into three parts. The '''Annotation Overview''' presents the basic information about the feature. '''Reasons for Current Assignment''' reflect why the feature was assigned with the current functional role. The third part is a '''Compare Regions View''' showing the region of the feature in context to its own and related genomes. If you are logged in and the feature belongs to your private genome, this page will have additional options for you to annotate the feature. These are described [[SEED_Viewer_Manual/Editing_Capabilities/Annotation|here]]. === The Annotation Overview === The feature ID and the genome it belongs to are shown in the header line of this part of the page. They link to [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] and the [[SEED_Viewer_Manual/OrganismPage|Organism Page]], respectively. The '''current annotation''' depicts the functional role that is currently assigned to the feature. As annotations can be changed by users, you have the option to view an annotation history by pressing the '''show''' button in the cell '''annotation history''' some rows below. It will open a small table listing the date, the curator and the annotation that was made for each entry. As the genome name for the feature is already presented in the header of this section, we additionally show the '''taxonomy id''' for that genome in the overview. The link will lead to the Taxonomy Browser at the NCBI showing the taxonomy information for that genome. Behind the taxonomy for the genome you can find the '''contig''' the feature can be found on. The '''internal links''' you can see in the next row are leading to different pages containing other views and information for the feature. The [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] ('''genome browser''') displays the feature in the context of its genome. '''evidence''' leads to the [[SEED_Viewer_Manual/Evidence|Evidence]] page showing evidence for the annotation of the feature in form of [[Glossary/Similarities|Similarities]] and protein domains. Downloading the actual sequence for the feature is possible using the [[SEED_Viewer_Manual/ShowSeqs|Sequence Page]] ('''sequence''') link. At '''PubMed Links''' you can see the PubMed IDs to papers linked to the NCBI Entrez Database. The PubMed IDs shown are direct literature links attached directly to a feature, so-called '''dlits'''. '''FIGfams''' are protein families based on the subsystems technology. If you find an entry in this fields, the feature is part of the stated FIGfam. The link leads to the [[SEED_Viewer_Manual/FIGfams|FIGfam Viewer]]. '''database cross references''' link the feature to its entries (Aliases) in other databases like UniProt, GenBANK and many others. [[Image:AnnotationFeat.png]] === Reasons for Current Assignment === [[Image:AnnotationAnnot.png]] === Compare Regions === [[Image:AnnotationComp.png]] 13ad4e0d9dcb50e4f83722738e4fef847cbdeaf8 1991 1990 2008-11-21T14:32:44Z DanielaBartels 10 /* The Annotation Overview */ wikitext text/x-wiki == Annotation == The Annotation page shows a variaty of information about a single feature like a protein or an RNA. The page is roughly divided into three parts. The '''Annotation Overview''' presents the basic information about the feature. '''Reasons for Current Assignment''' reflect why the feature was assigned with the current functional role. The third part is a '''Compare Regions View''' showing the region of the feature in context to its own and related genomes. If you are logged in and the feature belongs to your private genome, this page will have additional options for you to annotate the feature. These are described [[SEED_Viewer_Manual/Editing_Capabilities/Annotation|here]]. === The Annotation Overview === The feature ID and the genome it belongs to are shown in the header line of this part of the page. They link to [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] and the [[SEED_Viewer_Manual/OrganismPage|Organism Page]], respectively. The '''current annotation''' depicts the functional role that is currently assigned to the feature. As annotations can be changed by users, you have the option to view an annotation history by pressing the '''show''' button in the cell '''annotation history''' some rows below. It will open a small table listing the date, the curator and the annotation that was made for each entry. As the genome name for the feature is already presented in the header of this section, we additionally show the '''taxonomy id''' for that genome in the overview. The link will lead to the Taxonomy Browser at the NCBI showing the taxonomy information for that genome. Behind the taxonomy for the genome you can find the '''contig''' the feature can be found on. The '''internal links''' you can see in the next row are leading to different pages containing other views and information for the feature. The [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] ('''genome browser''') displays the feature in the context of its genome. '''evidence''' leads to the [[SEED_Viewer_Manual/Evidence|Evidence]] page showing evidence for the annotation of the feature in form of [[Glossary/Similarities|Similarities]] and protein domains. Downloading the actual sequence for the feature is possible using the [[SEED_Viewer_Manual/ShowSeqs|Sequence Page]] ('''sequence''') link. Behind the external links you find a link to the '''ACH''' essentially identical genes. This link leads to the [[AnnotationClearingHouse|Annotation Clearing House]], a collection of proteins from many different sources. Proteins that have essentially the same sequence are grouped. For a given ID, you can see all IDs from different sources that belong to this group. At '''PubMed Links''' you can see the PubMed IDs to papers linked to the NCBI Entrez Database. The PubMed IDs shown are direct literature links attached directly to a feature, so-called '''dlits'''. '''FIGfams''' are protein families based on the subsystems technology. If you find an entry in this fields, the feature is part of the stated FIGfam. The link leads to the [[SEED_Viewer_Manual/FIGfams|FIGfam Viewer]]. '''database cross references''' link the feature to its entries (Aliases) in other databases like UniProt, GenBANK and many others. To gain more information about a feature, you can run different tools (e.g. PSI-BLAST, InterPro and many others) on your feature. Select a tool and press the button '''run tool'''. [[Image:AnnotationFeat.png]] === Reasons for Current Assignment === [[Image:AnnotationAnnot.png]] === Compare Regions === [[Image:AnnotationComp.png]] 847c0a14446e35208446c1641269e7db5322753e 1992 1991 2008-11-21T14:43:13Z DanielaBartels 10 /* Reasons for Current Assignment */ wikitext text/x-wiki == Annotation == The Annotation page shows a variaty of information about a single feature like a protein or an RNA. The page is roughly divided into three parts. The '''Annotation Overview''' presents the basic information about the feature. '''Reasons for Current Assignment''' reflect why the feature was assigned with the current functional role. The third part is a '''Compare Regions View''' showing the region of the feature in context to its own and related genomes. If you are logged in and the feature belongs to your private genome, this page will have additional options for you to annotate the feature. These are described [[SEED_Viewer_Manual/Editing_Capabilities/Annotation|here]]. === The Annotation Overview === The feature ID and the genome it belongs to are shown in the header line of this part of the page. They link to [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] and the [[SEED_Viewer_Manual/OrganismPage|Organism Page]], respectively. The '''current annotation''' depicts the functional role that is currently assigned to the feature. As annotations can be changed by users, you have the option to view an annotation history by pressing the '''show''' button in the cell '''annotation history''' some rows below. It will open a small table listing the date, the curator and the annotation that was made for each entry. As the genome name for the feature is already presented in the header of this section, we additionally show the '''taxonomy id''' for that genome in the overview. The link will lead to the Taxonomy Browser at the NCBI showing the taxonomy information for that genome. Behind the taxonomy for the genome you can find the '''contig''' the feature can be found on. The '''internal links''' you can see in the next row are leading to different pages containing other views and information for the feature. The [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] ('''genome browser''') displays the feature in the context of its genome. '''evidence''' leads to the [[SEED_Viewer_Manual/Evidence|Evidence]] page showing evidence for the annotation of the feature in form of [[Glossary/Similarities|Similarities]] and protein domains. Downloading the actual sequence for the feature is possible using the [[SEED_Viewer_Manual/ShowSeqs|Sequence Page]] ('''sequence''') link. Behind the external links you find a link to the '''ACH''' essentially identical genes. This link leads to the [[AnnotationClearingHouse|Annotation Clearing House]], a collection of proteins from many different sources. Proteins that have essentially the same sequence are grouped. For a given ID, you can see all IDs from different sources that belong to this group. At '''PubMed Links''' you can see the PubMed IDs to papers linked to the NCBI Entrez Database. The PubMed IDs shown are direct literature links attached directly to a feature, so-called '''dlits'''. '''FIGfams''' are protein families based on the subsystems technology. If you find an entry in this fields, the feature is part of the stated FIGfam. The link leads to the [[SEED_Viewer_Manual/FIGfams|FIGfam Viewer]]. '''database cross references''' link the feature to its entries (Aliases) in other databases like UniProt, GenBANK and many others. To gain more information about a feature, you can run different tools (e.g. PSI-BLAST, InterPro and many others) on your feature. Select a tool and press the button '''run tool'''. [[Image:AnnotationFeat.png]] === Reasons for Current Assignment === To gain a clue about what evidence an assignment of a functional role to your feature is based on, the text in '''Reasons for Current Assignment summarizes important information supporting the annotation. Additional to the information in the overview table, a list of indirect literature ('''ilits''') is decribed in the text. Those are based on direct literature to similar features that have the same functional role. [[Image:AnnotationAnnot.png]] === Compare Regions === [[Image:AnnotationComp.png]] daf0c7b5a7c44c06de0c9a852df54702b03ec649 1993 1992 2008-11-21T14:43:33Z DanielaBartels 10 /* Reasons for Current Assignment */ wikitext text/x-wiki == Annotation == The Annotation page shows a variaty of information about a single feature like a protein or an RNA. The page is roughly divided into three parts. The '''Annotation Overview''' presents the basic information about the feature. '''Reasons for Current Assignment''' reflect why the feature was assigned with the current functional role. The third part is a '''Compare Regions View''' showing the region of the feature in context to its own and related genomes. If you are logged in and the feature belongs to your private genome, this page will have additional options for you to annotate the feature. These are described [[SEED_Viewer_Manual/Editing_Capabilities/Annotation|here]]. === The Annotation Overview === The feature ID and the genome it belongs to are shown in the header line of this part of the page. They link to [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] and the [[SEED_Viewer_Manual/OrganismPage|Organism Page]], respectively. The '''current annotation''' depicts the functional role that is currently assigned to the feature. As annotations can be changed by users, you have the option to view an annotation history by pressing the '''show''' button in the cell '''annotation history''' some rows below. It will open a small table listing the date, the curator and the annotation that was made for each entry. As the genome name for the feature is already presented in the header of this section, we additionally show the '''taxonomy id''' for that genome in the overview. The link will lead to the Taxonomy Browser at the NCBI showing the taxonomy information for that genome. Behind the taxonomy for the genome you can find the '''contig''' the feature can be found on. The '''internal links''' you can see in the next row are leading to different pages containing other views and information for the feature. The [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] ('''genome browser''') displays the feature in the context of its genome. '''evidence''' leads to the [[SEED_Viewer_Manual/Evidence|Evidence]] page showing evidence for the annotation of the feature in form of [[Glossary/Similarities|Similarities]] and protein domains. Downloading the actual sequence for the feature is possible using the [[SEED_Viewer_Manual/ShowSeqs|Sequence Page]] ('''sequence''') link. Behind the external links you find a link to the '''ACH''' essentially identical genes. This link leads to the [[AnnotationClearingHouse|Annotation Clearing House]], a collection of proteins from many different sources. Proteins that have essentially the same sequence are grouped. For a given ID, you can see all IDs from different sources that belong to this group. At '''PubMed Links''' you can see the PubMed IDs to papers linked to the NCBI Entrez Database. The PubMed IDs shown are direct literature links attached directly to a feature, so-called '''dlits'''. '''FIGfams''' are protein families based on the subsystems technology. If you find an entry in this fields, the feature is part of the stated FIGfam. The link leads to the [[SEED_Viewer_Manual/FIGfams|FIGfam Viewer]]. '''database cross references''' link the feature to its entries (Aliases) in other databases like UniProt, GenBANK and many others. To gain more information about a feature, you can run different tools (e.g. PSI-BLAST, InterPro and many others) on your feature. Select a tool and press the button '''run tool'''. [[Image:AnnotationFeat.png]] === Reasons for Current Assignment === To gain a clue about what evidence an assignment of a functional role to your feature is based on, the text in '''Reasons for Current Assignment''' summarizes important information supporting the annotation. Additional to the information in the overview table, a list of indirect literature ('''ilits''') is decribed in the text. Those are based on direct literature to similar features that have the same functional role. [[Image:AnnotationAnnot.png]] === Compare Regions === [[Image:AnnotationComp.png]] 4bf98ed5813bbe67227006fea4ae2aea38a3ba97 1994 1993 2008-11-21T14:47:13Z DanielaBartels 10 /* Compare Regions */ wikitext text/x-wiki == Annotation == The Annotation page shows a variaty of information about a single feature like a protein or an RNA. The page is roughly divided into three parts. The '''Annotation Overview''' presents the basic information about the feature. '''Reasons for Current Assignment''' reflect why the feature was assigned with the current functional role. The third part is a '''Compare Regions View''' showing the region of the feature in context to its own and related genomes. If you are logged in and the feature belongs to your private genome, this page will have additional options for you to annotate the feature. These are described [[SEED_Viewer_Manual/Editing_Capabilities/Annotation|here]]. === The Annotation Overview === The feature ID and the genome it belongs to are shown in the header line of this part of the page. They link to [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] and the [[SEED_Viewer_Manual/OrganismPage|Organism Page]], respectively. The '''current annotation''' depicts the functional role that is currently assigned to the feature. As annotations can be changed by users, you have the option to view an annotation history by pressing the '''show''' button in the cell '''annotation history''' some rows below. It will open a small table listing the date, the curator and the annotation that was made for each entry. As the genome name for the feature is already presented in the header of this section, we additionally show the '''taxonomy id''' for that genome in the overview. The link will lead to the Taxonomy Browser at the NCBI showing the taxonomy information for that genome. Behind the taxonomy for the genome you can find the '''contig''' the feature can be found on. The '''internal links''' you can see in the next row are leading to different pages containing other views and information for the feature. The [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] ('''genome browser''') displays the feature in the context of its genome. '''evidence''' leads to the [[SEED_Viewer_Manual/Evidence|Evidence]] page showing evidence for the annotation of the feature in form of [[Glossary/Similarities|Similarities]] and protein domains. Downloading the actual sequence for the feature is possible using the [[SEED_Viewer_Manual/ShowSeqs|Sequence Page]] ('''sequence''') link. Behind the external links you find a link to the '''ACH''' essentially identical genes. This link leads to the [[AnnotationClearingHouse|Annotation Clearing House]], a collection of proteins from many different sources. Proteins that have essentially the same sequence are grouped. For a given ID, you can see all IDs from different sources that belong to this group. At '''PubMed Links''' you can see the PubMed IDs to papers linked to the NCBI Entrez Database. The PubMed IDs shown are direct literature links attached directly to a feature, so-called '''dlits'''. '''FIGfams''' are protein families based on the subsystems technology. If you find an entry in this fields, the feature is part of the stated FIGfam. The link leads to the [[SEED_Viewer_Manual/FIGfams|FIGfam Viewer]]. '''database cross references''' link the feature to its entries (Aliases) in other databases like UniProt, GenBANK and many others. To gain more information about a feature, you can run different tools (e.g. PSI-BLAST, InterPro and many others) on your feature. Select a tool and press the button '''run tool'''. [[Image:AnnotationFeat.png]] === Reasons for Current Assignment === To gain a clue about what evidence an assignment of a functional role to your feature is based on, the text in '''Reasons for Current Assignment''' summarizes important information supporting the annotation. Additional to the information in the overview table, a list of indirect literature ('''ilits''') is decribed in the text. Those are based on direct literature to similar features that have the same functional role. [[Image:AnnotationAnnot.png]] === Compare Regions === The first line of the '''Compare Regions''' is a graphical display of the region of the feature its genome. The graph is centered on the feature, which is always colored red. [[Image:AnnotationComp.png]] 366e3fe6627e97beb66c431ae1ef1e4258ae5d62 1995 1994 2008-11-21T15:00:56Z DanielaBartels 10 /* Compare Regions */ wikitext text/x-wiki == Annotation == The Annotation page shows a variaty of information about a single feature like a protein or an RNA. The page is roughly divided into three parts. The '''Annotation Overview''' presents the basic information about the feature. '''Reasons for Current Assignment''' reflect why the feature was assigned with the current functional role. The third part is a '''Compare Regions View''' showing the region of the feature in context to its own and related genomes. If you are logged in and the feature belongs to your private genome, this page will have additional options for you to annotate the feature. These are described [[SEED_Viewer_Manual/Editing_Capabilities/Annotation|here]]. === The Annotation Overview === The feature ID and the genome it belongs to are shown in the header line of this part of the page. They link to [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] and the [[SEED_Viewer_Manual/OrganismPage|Organism Page]], respectively. The '''current annotation''' depicts the functional role that is currently assigned to the feature. As annotations can be changed by users, you have the option to view an annotation history by pressing the '''show''' button in the cell '''annotation history''' some rows below. It will open a small table listing the date, the curator and the annotation that was made for each entry. As the genome name for the feature is already presented in the header of this section, we additionally show the '''taxonomy id''' for that genome in the overview. The link will lead to the Taxonomy Browser at the NCBI showing the taxonomy information for that genome. Behind the taxonomy for the genome you can find the '''contig''' the feature can be found on. The '''internal links''' you can see in the next row are leading to different pages containing other views and information for the feature. The [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] ('''genome browser''') displays the feature in the context of its genome. '''evidence''' leads to the [[SEED_Viewer_Manual/Evidence|Evidence]] page showing evidence for the annotation of the feature in form of [[Glossary/Similarities|Similarities]] and protein domains. Downloading the actual sequence for the feature is possible using the [[SEED_Viewer_Manual/ShowSeqs|Sequence Page]] ('''sequence''') link. Behind the external links you find a link to the '''ACH''' essentially identical genes. This link leads to the [[AnnotationClearingHouse|Annotation Clearing House]], a collection of proteins from many different sources. Proteins that have essentially the same sequence are grouped. For a given ID, you can see all IDs from different sources that belong to this group. At '''PubMed Links''' you can see the PubMed IDs to papers linked to the NCBI Entrez Database. The PubMed IDs shown are direct literature links attached directly to a feature, so-called '''dlits'''. '''FIGfams''' are protein families based on the subsystems technology. If you find an entry in this fields, the feature is part of the stated FIGfam. The link leads to the [[SEED_Viewer_Manual/FIGfams|FIGfam Viewer]]. '''database cross references''' link the feature to its entries (Aliases) in other databases like UniProt, GenBANK and many others. To gain more information about a feature, you can run different tools (e.g. PSI-BLAST, InterPro and many others) on your feature. Select a tool and press the button '''run tool'''. [[Image:AnnotationFeat.png]] === Reasons for Current Assignment === To gain a clue about what evidence an assignment of a functional role to your feature is based on, the text in '''Reasons for Current Assignment''' summarizes important information supporting the annotation. Additional to the information in the overview table, a list of indirect literature ('''ilits''') is decribed in the text. Those are based on direct literature to similar features that have the same functional role. [[Image:AnnotationAnnot.png]] === Compare Regions === The first line of the '''Compare Regions''' is a graphical display of the region of the feature its genome. All proteins are shown as colored arrows, where the direction depicts the strand of the feature. RNAs and other features are small boxes on the line. If two features overlap, the overlapping will be drawn on an (invisible) second line. The graph is centered on the selected feature (numbered 1), which is always colored red. Below you find the same region for orthologs in other (related) organisms, also colored in red. The colors of the other features (as well as the numbers) also represent ortholog (or sometimes also paralog) features. Whenever there are at least two ortholog or paralog features, a color (and a number) is assigned to them. [[Image:AnnotationComp.png]] 087727f3458bd2005a6e0077bbac5258611a48fe 1996 1995 2008-11-24T11:27:37Z DanielaBartels 10 /* Compare Regions */ wikitext text/x-wiki == Annotation == The Annotation page shows a variaty of information about a single feature like a protein or an RNA. The page is roughly divided into three parts. The '''Annotation Overview''' presents the basic information about the feature. '''Reasons for Current Assignment''' reflect why the feature was assigned with the current functional role. The third part is a '''Compare Regions View''' showing the region of the feature in context to its own and related genomes. If you are logged in and the feature belongs to your private genome, this page will have additional options for you to annotate the feature. These are described [[SEED_Viewer_Manual/Editing_Capabilities/Annotation|here]]. === The Annotation Overview === The feature ID and the genome it belongs to are shown in the header line of this part of the page. They link to [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] and the [[SEED_Viewer_Manual/OrganismPage|Organism Page]], respectively. The '''current annotation''' depicts the functional role that is currently assigned to the feature. As annotations can be changed by users, you have the option to view an annotation history by pressing the '''show''' button in the cell '''annotation history''' some rows below. It will open a small table listing the date, the curator and the annotation that was made for each entry. As the genome name for the feature is already presented in the header of this section, we additionally show the '''taxonomy id''' for that genome in the overview. The link will lead to the Taxonomy Browser at the NCBI showing the taxonomy information for that genome. Behind the taxonomy for the genome you can find the '''contig''' the feature can be found on. The '''internal links''' you can see in the next row are leading to different pages containing other views and information for the feature. The [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] ('''genome browser''') displays the feature in the context of its genome. '''evidence''' leads to the [[SEED_Viewer_Manual/Evidence|Evidence]] page showing evidence for the annotation of the feature in form of [[Glossary/Similarities|Similarities]] and protein domains. Downloading the actual sequence for the feature is possible using the [[SEED_Viewer_Manual/ShowSeqs|Sequence Page]] ('''sequence''') link. Behind the external links you find a link to the '''ACH''' essentially identical genes. This link leads to the [[AnnotationClearingHouse|Annotation Clearing House]], a collection of proteins from many different sources. Proteins that have essentially the same sequence are grouped. For a given ID, you can see all IDs from different sources that belong to this group. At '''PubMed Links''' you can see the PubMed IDs to papers linked to the NCBI Entrez Database. The PubMed IDs shown are direct literature links attached directly to a feature, so-called '''dlits'''. '''FIGfams''' are protein families based on the subsystems technology. If you find an entry in this fields, the feature is part of the stated FIGfam. The link leads to the [[SEED_Viewer_Manual/FIGfams|FIGfam Viewer]]. '''database cross references''' link the feature to its entries (Aliases) in other databases like UniProt, GenBANK and many others. To gain more information about a feature, you can run different tools (e.g. PSI-BLAST, InterPro and many others) on your feature. Select a tool and press the button '''run tool'''. [[Image:AnnotationFeat.png]] === Reasons for Current Assignment === To gain a clue about what evidence an assignment of a functional role to your feature is based on, the text in '''Reasons for Current Assignment''' summarizes important information supporting the annotation. Additional to the information in the overview table, a list of indirect literature ('''ilits''') is decribed in the text. Those are based on direct literature to similar features that have the same functional role. [[Image:AnnotationAnnot.png]] === Compare Regions === The first line of the '''Compare Regions''' is a graphical display of the region of the feature its genome. All proteins are shown as colored arrows, where the direction depicts the strand of the feature. RNAs and other features are small boxes on the line. If two features overlap, the overlapping will be drawn on an (invisible) second line. The graph is centered on the selected feature (numbered 1), which is always colored red. Below you find the same region for orthologs in other (related) organisms, also colored in red. The colors of the other features (as well as the numbers) also represent ortholog (or sometimes also paralog) features. Whenever there are at least two ortholog or paralog features of a kind, a color (and a number) is assigned to them. [[Image:AnnotationComp.png]] 85835fd2214cb3d5ca0791cba33028b94e3f4d6f 1997 1996 2008-11-24T11:28:38Z DanielaBartels 10 /* Compare Regions */ wikitext text/x-wiki == Annotation == The Annotation page shows a variaty of information about a single feature like a protein or an RNA. The page is roughly divided into three parts. The '''Annotation Overview''' presents the basic information about the feature. '''Reasons for Current Assignment''' reflect why the feature was assigned with the current functional role. The third part is a '''Compare Regions View''' showing the region of the feature in context to its own and related genomes. If you are logged in and the feature belongs to your private genome, this page will have additional options for you to annotate the feature. These are described [[SEED_Viewer_Manual/Editing_Capabilities/Annotation|here]]. === The Annotation Overview === The feature ID and the genome it belongs to are shown in the header line of this part of the page. They link to [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] and the [[SEED_Viewer_Manual/OrganismPage|Organism Page]], respectively. The '''current annotation''' depicts the functional role that is currently assigned to the feature. As annotations can be changed by users, you have the option to view an annotation history by pressing the '''show''' button in the cell '''annotation history''' some rows below. It will open a small table listing the date, the curator and the annotation that was made for each entry. As the genome name for the feature is already presented in the header of this section, we additionally show the '''taxonomy id''' for that genome in the overview. The link will lead to the Taxonomy Browser at the NCBI showing the taxonomy information for that genome. Behind the taxonomy for the genome you can find the '''contig''' the feature can be found on. The '''internal links''' you can see in the next row are leading to different pages containing other views and information for the feature. The [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] ('''genome browser''') displays the feature in the context of its genome. '''evidence''' leads to the [[SEED_Viewer_Manual/Evidence|Evidence]] page showing evidence for the annotation of the feature in form of [[Glossary/Similarities|Similarities]] and protein domains. Downloading the actual sequence for the feature is possible using the [[SEED_Viewer_Manual/ShowSeqs|Sequence Page]] ('''sequence''') link. Behind the external links you find a link to the '''ACH''' essentially identical genes. This link leads to the [[AnnotationClearingHouse|Annotation Clearing House]], a collection of proteins from many different sources. Proteins that have essentially the same sequence are grouped. For a given ID, you can see all IDs from different sources that belong to this group. At '''PubMed Links''' you can see the PubMed IDs to papers linked to the NCBI Entrez Database. The PubMed IDs shown are direct literature links attached directly to a feature, so-called '''dlits'''. '''FIGfams''' are protein families based on the subsystems technology. If you find an entry in this fields, the feature is part of the stated FIGfam. The link leads to the [[SEED_Viewer_Manual/FIGfams|FIGfam Viewer]]. '''database cross references''' link the feature to its entries (Aliases) in other databases like UniProt, GenBANK and many others. To gain more information about a feature, you can run different tools (e.g. PSI-BLAST, InterPro and many others) on your feature. Select a tool and press the button '''run tool'''. [[Image:AnnotationFeat.png]] === Reasons for Current Assignment === To gain a clue about what evidence an assignment of a functional role to your feature is based on, the text in '''Reasons for Current Assignment''' summarizes important information supporting the annotation. Additional to the information in the overview table, a list of indirect literature ('''ilits''') is decribed in the text. Those are based on direct literature to similar features that have the same functional role. [[Image:AnnotationAnnot.png]] === Compare Regions === The first line of the '''Compare Regions''' is a graphical display of the region of the feature its genome. All proteins are shown as colored arrows, where the direction depicts the strand of the feature. RNAs and other features are small boxes on the line. If two features overlap, the overlapping will be drawn on an (invisible) second line. The graph is centered on the selected feature (numbered 1), which is always colored red. Below you find the same region for orthologs in other (related) organisms, also colored in red. The colors of the other features (as well as the numbers) also represent ortholog (or sometimes also paralog) features. Whenever there are at least two ortholog or paralog features of a kind, a color (and a number) is assigned to them. [[Image:AnnotationComp.png]] [[Image:AnnotationTabl.png]] 6acd117581dc77be3cc37e39903e6971b66d095b 1999 1997 2008-11-24T11:36:03Z DanielaBartels 10 /* Compare Regions */ wikitext text/x-wiki == Annotation == The Annotation page shows a variaty of information about a single feature like a protein or an RNA. The page is roughly divided into three parts. The '''Annotation Overview''' presents the basic information about the feature. '''Reasons for Current Assignment''' reflect why the feature was assigned with the current functional role. The third part is a '''Compare Regions View''' showing the region of the feature in context to its own and related genomes. If you are logged in and the feature belongs to your private genome, this page will have additional options for you to annotate the feature. These are described [[SEED_Viewer_Manual/Editing_Capabilities/Annotation|here]]. === The Annotation Overview === The feature ID and the genome it belongs to are shown in the header line of this part of the page. They link to [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] and the [[SEED_Viewer_Manual/OrganismPage|Organism Page]], respectively. The '''current annotation''' depicts the functional role that is currently assigned to the feature. As annotations can be changed by users, you have the option to view an annotation history by pressing the '''show''' button in the cell '''annotation history''' some rows below. It will open a small table listing the date, the curator and the annotation that was made for each entry. As the genome name for the feature is already presented in the header of this section, we additionally show the '''taxonomy id''' for that genome in the overview. The link will lead to the Taxonomy Browser at the NCBI showing the taxonomy information for that genome. Behind the taxonomy for the genome you can find the '''contig''' the feature can be found on. The '''internal links''' you can see in the next row are leading to different pages containing other views and information for the feature. The [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] ('''genome browser''') displays the feature in the context of its genome. '''evidence''' leads to the [[SEED_Viewer_Manual/Evidence|Evidence]] page showing evidence for the annotation of the feature in form of [[Glossary/Similarities|Similarities]] and protein domains. Downloading the actual sequence for the feature is possible using the [[SEED_Viewer_Manual/ShowSeqs|Sequence Page]] ('''sequence''') link. Behind the external links you find a link to the '''ACH''' essentially identical genes. This link leads to the [[AnnotationClearingHouse|Annotation Clearing House]], a collection of proteins from many different sources. Proteins that have essentially the same sequence are grouped. For a given ID, you can see all IDs from different sources that belong to this group. At '''PubMed Links''' you can see the PubMed IDs to papers linked to the NCBI Entrez Database. The PubMed IDs shown are direct literature links attached directly to a feature, so-called '''dlits'''. '''FIGfams''' are protein families based on the subsystems technology. If you find an entry in this fields, the feature is part of the stated FIGfam. The link leads to the [[SEED_Viewer_Manual/FIGfams|FIGfam Viewer]]. '''database cross references''' link the feature to its entries (Aliases) in other databases like UniProt, GenBANK and many others. To gain more information about a feature, you can run different tools (e.g. PSI-BLAST, InterPro and many others) on your feature. Select a tool and press the button '''run tool'''. [[Image:AnnotationFeat.png]] === Reasons for Current Assignment === To gain a clue about what evidence an assignment of a functional role to your feature is based on, the text in '''Reasons for Current Assignment''' summarizes important information supporting the annotation. Additional to the information in the overview table, a list of indirect literature ('''ilits''') is decribed in the text. Those are based on direct literature to similar features that have the same functional role. [[Image:AnnotationAnnot.png]] === Compare Regions === The first line of the '''Compare Regions''' is a graphical display of the region of the feature its genome. All proteins are shown as colored arrows, where the direction depicts the strand of the feature. RNAs and other features are small boxes on the line. If two features overlap, the overlapping will be drawn on an (invisible) second line. The graph is centered on the selected feature (numbered 1), which is always colored red. Below you find the same region for orthologs in other (related) organisms, also colored in red. The colors of the other features (as well as the numbers) also represent ortholog (or sometimes also paralog) features. Whenever there are at least two ortholog or paralog features of a kind, a color (and a number) is assigned to them. '''Display Options''' are divided into two ''Regular'' and ''Advanced''. In the '''Regular''' options, you can change the ''Region Size'' and the ''Number of Regions''. Changing the '''Region Size''' enables to zoom in or out of the region. [[Image:AnnotationComp.png]] [[Image:AnnotationTabl.png]] 5350d80ede8c8ed2b09af459b02e17727facc7a2 2000 1999 2008-11-24T11:40:27Z DanielaBartels 10 /* Compare Regions */ wikitext text/x-wiki == Annotation == The Annotation page shows a variaty of information about a single feature like a protein or an RNA. The page is roughly divided into three parts. The '''Annotation Overview''' presents the basic information about the feature. '''Reasons for Current Assignment''' reflect why the feature was assigned with the current functional role. The third part is a '''Compare Regions View''' showing the region of the feature in context to its own and related genomes. If you are logged in and the feature belongs to your private genome, this page will have additional options for you to annotate the feature. These are described [[SEED_Viewer_Manual/Editing_Capabilities/Annotation|here]]. === The Annotation Overview === The feature ID and the genome it belongs to are shown in the header line of this part of the page. They link to [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] and the [[SEED_Viewer_Manual/OrganismPage|Organism Page]], respectively. The '''current annotation''' depicts the functional role that is currently assigned to the feature. As annotations can be changed by users, you have the option to view an annotation history by pressing the '''show''' button in the cell '''annotation history''' some rows below. It will open a small table listing the date, the curator and the annotation that was made for each entry. As the genome name for the feature is already presented in the header of this section, we additionally show the '''taxonomy id''' for that genome in the overview. The link will lead to the Taxonomy Browser at the NCBI showing the taxonomy information for that genome. Behind the taxonomy for the genome you can find the '''contig''' the feature can be found on. The '''internal links''' you can see in the next row are leading to different pages containing other views and information for the feature. The [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] ('''genome browser''') displays the feature in the context of its genome. '''evidence''' leads to the [[SEED_Viewer_Manual/Evidence|Evidence]] page showing evidence for the annotation of the feature in form of [[Glossary/Similarities|Similarities]] and protein domains. Downloading the actual sequence for the feature is possible using the [[SEED_Viewer_Manual/ShowSeqs|Sequence Page]] ('''sequence''') link. Behind the external links you find a link to the '''ACH''' essentially identical genes. This link leads to the [[AnnotationClearingHouse|Annotation Clearing House]], a collection of proteins from many different sources. Proteins that have essentially the same sequence are grouped. For a given ID, you can see all IDs from different sources that belong to this group. At '''PubMed Links''' you can see the PubMed IDs to papers linked to the NCBI Entrez Database. The PubMed IDs shown are direct literature links attached directly to a feature, so-called '''dlits'''. '''FIGfams''' are protein families based on the subsystems technology. If you find an entry in this fields, the feature is part of the stated FIGfam. The link leads to the [[SEED_Viewer_Manual/FIGfams|FIGfam Viewer]]. '''database cross references''' link the feature to its entries (Aliases) in other databases like UniProt, GenBANK and many others. To gain more information about a feature, you can run different tools (e.g. PSI-BLAST, InterPro and many others) on your feature. Select a tool and press the button '''run tool'''. [[Image:AnnotationFeat.png]] === Reasons for Current Assignment === To gain a clue about what evidence an assignment of a functional role to your feature is based on, the text in '''Reasons for Current Assignment''' summarizes important information supporting the annotation. Additional to the information in the overview table, a list of indirect literature ('''ilits''') is decribed in the text. Those are based on direct literature to similar features that have the same functional role. [[Image:AnnotationAnnot.png]] === Compare Regions === The first line of the '''Compare Regions''' is a graphical display of the region of the feature its genome. All proteins are shown as colored arrows, where the direction depicts the strand of the feature. RNAs and other features are small boxes on the line. If two features overlap, the overlapping will be drawn on an (invisible) second line. The graph is centered on the selected feature (numbered 1), which is always colored red. Below you find the same region for orthologs in other (related) organisms, also colored in red. The colors of the other features (as well as the numbers) also represent ortholog (or sometimes also paralog) features. Whenever there are at least two ortholog or paralog features of a kind, a color (and a number) is assigned to them. '''Display Options''' are divided into two ''Regular'' and ''Advanced''. In the '''Regular''' options, you can change the ''Region Size'' and the ''Number of Regions''. Changing the '''Region Size''' enables to zoom in or out of the region. Changing the '''Number of Regions''' will add or remove genomes to your display. The numbers that you put in for these values will be saved as [[SEED_Viewer_Manual/Preferences|preferences]]. [[Image:AnnotationComp.png]] [[Image:AnnotationTabl.png]] fb5398f4670ca43f5b06c71e3a09175745f6aa8b 2001 2000 2008-11-24T11:43:01Z DanielaBartels 10 /* Compare Regions */ wikitext text/x-wiki == Annotation == The Annotation page shows a variaty of information about a single feature like a protein or an RNA. The page is roughly divided into three parts. The '''Annotation Overview''' presents the basic information about the feature. '''Reasons for Current Assignment''' reflect why the feature was assigned with the current functional role. The third part is a '''Compare Regions View''' showing the region of the feature in context to its own and related genomes. If you are logged in and the feature belongs to your private genome, this page will have additional options for you to annotate the feature. These are described [[SEED_Viewer_Manual/Editing_Capabilities/Annotation|here]]. === The Annotation Overview === The feature ID and the genome it belongs to are shown in the header line of this part of the page. They link to [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] and the [[SEED_Viewer_Manual/OrganismPage|Organism Page]], respectively. The '''current annotation''' depicts the functional role that is currently assigned to the feature. As annotations can be changed by users, you have the option to view an annotation history by pressing the '''show''' button in the cell '''annotation history''' some rows below. It will open a small table listing the date, the curator and the annotation that was made for each entry. As the genome name for the feature is already presented in the header of this section, we additionally show the '''taxonomy id''' for that genome in the overview. The link will lead to the Taxonomy Browser at the NCBI showing the taxonomy information for that genome. Behind the taxonomy for the genome you can find the '''contig''' the feature can be found on. The '''internal links''' you can see in the next row are leading to different pages containing other views and information for the feature. The [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] ('''genome browser''') displays the feature in the context of its genome. '''evidence''' leads to the [[SEED_Viewer_Manual/Evidence|Evidence]] page showing evidence for the annotation of the feature in form of [[Glossary/Similarities|Similarities]] and protein domains. Downloading the actual sequence for the feature is possible using the [[SEED_Viewer_Manual/ShowSeqs|Sequence Page]] ('''sequence''') link. Behind the external links you find a link to the '''ACH''' essentially identical genes. This link leads to the [[AnnotationClearingHouse|Annotation Clearing House]], a collection of proteins from many different sources. Proteins that have essentially the same sequence are grouped. For a given ID, you can see all IDs from different sources that belong to this group. At '''PubMed Links''' you can see the PubMed IDs to papers linked to the NCBI Entrez Database. The PubMed IDs shown are direct literature links attached directly to a feature, so-called '''dlits'''. '''FIGfams''' are protein families based on the subsystems technology. If you find an entry in this fields, the feature is part of the stated FIGfam. The link leads to the [[SEED_Viewer_Manual/FIGfams|FIGfam Viewer]]. '''database cross references''' link the feature to its entries (Aliases) in other databases like UniProt, GenBANK and many others. To gain more information about a feature, you can run different tools (e.g. PSI-BLAST, InterPro and many others) on your feature. Select a tool and press the button '''run tool'''. [[Image:AnnotationFeat.png]] === Reasons for Current Assignment === To gain a clue about what evidence an assignment of a functional role to your feature is based on, the text in '''Reasons for Current Assignment''' summarizes important information supporting the annotation. Additional to the information in the overview table, a list of indirect literature ('''ilits''') is decribed in the text. Those are based on direct literature to similar features that have the same functional role. [[Image:AnnotationAnnot.png]] === Compare Regions === The first line of the '''Compare Regions''' is a graphical display of the region of the feature its genome. All proteins are shown as colored arrows, where the direction depicts the strand of the feature. RNAs and other features are small boxes on the line. If two features overlap, the overlapping will be drawn on an (invisible) second line. The graph is centered on the selected feature (numbered 1), which is always colored red. Below you find the same region for orthologs in other (related) organisms, also colored in red. The colors of the other features (as well as the numbers) also represent ortholog (or sometimes also paralog) features. Whenever there are at least two ortholog or paralog features of a kind, a color (and a number) is assigned to them. '''Display Options''' are divided into two ''Regular'' and ''Advanced''. In the '''Regular''' options, you can change the ''Region Size'' and the ''Number of Regions''. Changing the '''Region Size''' enables to zoom in or out of the region. Changing the '''Number of Regions''' will add or remove genomes to your display. The numbers that you put in for these values will be saved as [[SEED_Viewer_Manual/Preferences|preferences]]. [[Image:AnnotationComp.png]] [[Image:AnnotationAdv.png]] [[Image:AnnotationTabl.png]] ce8d70248d10f6d71edd7d9e25aa8c0c17833a3c 2003 2001 2008-11-24T12:09:44Z DanielaBartels 10 /* Compare Regions */ wikitext text/x-wiki == Annotation == The Annotation page shows a variaty of information about a single feature like a protein or an RNA. The page is roughly divided into three parts. The '''Annotation Overview''' presents the basic information about the feature. '''Reasons for Current Assignment''' reflect why the feature was assigned with the current functional role. The third part is a '''Compare Regions View''' showing the region of the feature in context to its own and related genomes. If you are logged in and the feature belongs to your private genome, this page will have additional options for you to annotate the feature. These are described [[SEED_Viewer_Manual/Editing_Capabilities/Annotation|here]]. === The Annotation Overview === The feature ID and the genome it belongs to are shown in the header line of this part of the page. They link to [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] and the [[SEED_Viewer_Manual/OrganismPage|Organism Page]], respectively. The '''current annotation''' depicts the functional role that is currently assigned to the feature. As annotations can be changed by users, you have the option to view an annotation history by pressing the '''show''' button in the cell '''annotation history''' some rows below. It will open a small table listing the date, the curator and the annotation that was made for each entry. As the genome name for the feature is already presented in the header of this section, we additionally show the '''taxonomy id''' for that genome in the overview. The link will lead to the Taxonomy Browser at the NCBI showing the taxonomy information for that genome. Behind the taxonomy for the genome you can find the '''contig''' the feature can be found on. The '''internal links''' you can see in the next row are leading to different pages containing other views and information for the feature. The [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] ('''genome browser''') displays the feature in the context of its genome. '''evidence''' leads to the [[SEED_Viewer_Manual/Evidence|Evidence]] page showing evidence for the annotation of the feature in form of [[Glossary/Similarities|Similarities]] and protein domains. Downloading the actual sequence for the feature is possible using the [[SEED_Viewer_Manual/ShowSeqs|Sequence Page]] ('''sequence''') link. Behind the external links you find a link to the '''ACH''' essentially identical genes. This link leads to the [[AnnotationClearingHouse|Annotation Clearing House]], a collection of proteins from many different sources. Proteins that have essentially the same sequence are grouped. For a given ID, you can see all IDs from different sources that belong to this group. At '''PubMed Links''' you can see the PubMed IDs to papers linked to the NCBI Entrez Database. The PubMed IDs shown are direct literature links attached directly to a feature, so-called '''dlits'''. '''FIGfams''' are protein families based on the subsystems technology. If you find an entry in this fields, the feature is part of the stated FIGfam. The link leads to the [[SEED_Viewer_Manual/FIGfams|FIGfam Viewer]]. '''database cross references''' link the feature to its entries (Aliases) in other databases like UniProt, GenBANK and many others. To gain more information about a feature, you can run different tools (e.g. PSI-BLAST, InterPro and many others) on your feature. Select a tool and press the button '''run tool'''. [[Image:AnnotationFeat.png]] === Reasons for Current Assignment === To gain a clue about what evidence an assignment of a functional role to your feature is based on, the text in '''Reasons for Current Assignment''' summarizes important information supporting the annotation. Additional to the information in the overview table, a list of indirect literature ('''ilits''') is decribed in the text. Those are based on direct literature to similar features that have the same functional role. [[Image:AnnotationAnnot.png]] === Compare Regions === The first line of the '''Compare Regions''' is a graphical display of the region of the feature its genome. All proteins are shown as colored arrows, where the direction depicts the strand of the feature. RNAs and other features are small boxes on the line. If two features overlap, the overlapping will be drawn on an (invisible) second line. The graph is centered on the selected feature (numbered 1), which is always colored red. Below you find the same region for orthologs in other (related) organisms, also colored in red. The colors of the other features (as well as the numbers) also represent ortholog (or sometimes also paralog) features. Whenever there are at least two ortholog or paralog features of a kind, a color (and a number) is assigned to them. '''Display Options''' are divided into two ''Regular'' and ''Advanced''. In the '''Regular''' options, you can change the ''Region Size'' and the ''Number of Regions''. Changing the '''Region Size''' enables to zoom in or out of the region. Changing the '''Number of Regions''' will add or remove genomes to your display. Click '''update graphics''' to change the display. The numbers that you put in for these values will be saved as [[SEED_Viewer_Manual/Preferences|preferences]]. [[Image:AnnotationComp.png]] If you click '''Advanced''' options, you will see the default options that are used for the Compare Regions View. The '''Pinned CDS Selection''' refers to the chosen peg and its orthologs in other genomes. The selection of genomes to show in the graphics can be made by ''Similarity'' or ''PCH pin''. The default is '''Similarity''' and means that the genomes are chosen using the similarity of the selected genes to its orthologs in other genomes. [[Image:AnnotationAdv.png]] [[Image:AnnotationTabl.png]] a3a5640d09a9727fea75f102f34962080f1cf8b9 2004 2003 2008-11-24T12:14:32Z DanielaBartels 10 /* Compare Regions */ wikitext text/x-wiki == Annotation == The Annotation page shows a variaty of information about a single feature like a protein or an RNA. The page is roughly divided into three parts. The '''Annotation Overview''' presents the basic information about the feature. '''Reasons for Current Assignment''' reflect why the feature was assigned with the current functional role. The third part is a '''Compare Regions View''' showing the region of the feature in context to its own and related genomes. If you are logged in and the feature belongs to your private genome, this page will have additional options for you to annotate the feature. These are described [[SEED_Viewer_Manual/Editing_Capabilities/Annotation|here]]. === The Annotation Overview === The feature ID and the genome it belongs to are shown in the header line of this part of the page. They link to [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] and the [[SEED_Viewer_Manual/OrganismPage|Organism Page]], respectively. The '''current annotation''' depicts the functional role that is currently assigned to the feature. As annotations can be changed by users, you have the option to view an annotation history by pressing the '''show''' button in the cell '''annotation history''' some rows below. It will open a small table listing the date, the curator and the annotation that was made for each entry. As the genome name for the feature is already presented in the header of this section, we additionally show the '''taxonomy id''' for that genome in the overview. The link will lead to the Taxonomy Browser at the NCBI showing the taxonomy information for that genome. Behind the taxonomy for the genome you can find the '''contig''' the feature can be found on. The '''internal links''' you can see in the next row are leading to different pages containing other views and information for the feature. The [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] ('''genome browser''') displays the feature in the context of its genome. '''evidence''' leads to the [[SEED_Viewer_Manual/Evidence|Evidence]] page showing evidence for the annotation of the feature in form of [[Glossary/Similarities|Similarities]] and protein domains. Downloading the actual sequence for the feature is possible using the [[SEED_Viewer_Manual/ShowSeqs|Sequence Page]] ('''sequence''') link. Behind the external links you find a link to the '''ACH''' essentially identical genes. This link leads to the [[AnnotationClearingHouse|Annotation Clearing House]], a collection of proteins from many different sources. Proteins that have essentially the same sequence are grouped. For a given ID, you can see all IDs from different sources that belong to this group. At '''PubMed Links''' you can see the PubMed IDs to papers linked to the NCBI Entrez Database. The PubMed IDs shown are direct literature links attached directly to a feature, so-called '''dlits'''. '''FIGfams''' are protein families based on the subsystems technology. If you find an entry in this fields, the feature is part of the stated FIGfam. The link leads to the [[SEED_Viewer_Manual/FIGfams|FIGfam Viewer]]. '''database cross references''' link the feature to its entries (Aliases) in other databases like UniProt, GenBANK and many others. To gain more information about a feature, you can run different tools (e.g. PSI-BLAST, InterPro and many others) on your feature. Select a tool and press the button '''run tool'''. [[Image:AnnotationFeat.png]] === Reasons for Current Assignment === To gain a clue about what evidence an assignment of a functional role to your feature is based on, the text in '''Reasons for Current Assignment''' summarizes important information supporting the annotation. Additional to the information in the overview table, a list of indirect literature ('''ilits''') is decribed in the text. Those are based on direct literature to similar features that have the same functional role. [[Image:AnnotationAnnot.png]] === Compare Regions === The first line of the '''Compare Regions''' is a graphical display of the region of the feature its genome. All proteins are shown as colored arrows, where the direction depicts the strand of the feature. RNAs and other features are small boxes on the line. If two features overlap, the overlapping will be drawn on an (invisible) second line. The graph is centered on the selected feature (numbered 1), which is always colored red. Below you find the same region for orthologs in other (related) organisms, also colored in red. The colors of the other features (as well as the numbers) also represent ortholog (or sometimes also paralog) features. Whenever there are at least two ortholog or paralog features of a kind, a color (and a number) is assigned to them. '''Display Options''' are divided into two ''Regular'' and ''Advanced''. In the '''Regular''' options, you can change the ''Region Size'' and the ''Number of Regions''. Changing the '''Region Size''' enables to zoom in or out of the region. Changing the '''Number of Regions''' will add or remove genomes to your display. Click '''update graphics''' to change the display. The numbers that you put in for these values will be saved as [[SEED_Viewer_Manual/Preferences|preferences]]. [[Image:AnnotationComp.png]] If you click '''Advanced''' options, you will see the default options that are used for the Compare Regions View. The '''Pinned CDS Selection''' refers to the chosen peg and its orthologs in other genomes. The selection of genomes to show in the graphics can be made by ''Similarity'' or ''PCH pin''. The default is '''Similarity''' and means that the genomes are chosen using the similarity of the selected genes to its orthologs in other genomes. A '''PCH''' means a ''pair of close homologs''. [...] [[Image:AnnotationAdv.png]] [[Image:AnnotationTabl.png]] 096f01e63eb58349fb5792bd7a4522c6a42981a0 2005 2004 2008-11-24T12:26:43Z DanielaBartels 10 /* Compare Regions */ wikitext text/x-wiki == Annotation == The Annotation page shows a variaty of information about a single feature like a protein or an RNA. The page is roughly divided into three parts. The '''Annotation Overview''' presents the basic information about the feature. '''Reasons for Current Assignment''' reflect why the feature was assigned with the current functional role. The third part is a '''Compare Regions View''' showing the region of the feature in context to its own and related genomes. If you are logged in and the feature belongs to your private genome, this page will have additional options for you to annotate the feature. These are described [[SEED_Viewer_Manual/Editing_Capabilities/Annotation|here]]. === The Annotation Overview === The feature ID and the genome it belongs to are shown in the header line of this part of the page. They link to [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] and the [[SEED_Viewer_Manual/OrganismPage|Organism Page]], respectively. The '''current annotation''' depicts the functional role that is currently assigned to the feature. As annotations can be changed by users, you have the option to view an annotation history by pressing the '''show''' button in the cell '''annotation history''' some rows below. It will open a small table listing the date, the curator and the annotation that was made for each entry. As the genome name for the feature is already presented in the header of this section, we additionally show the '''taxonomy id''' for that genome in the overview. The link will lead to the Taxonomy Browser at the NCBI showing the taxonomy information for that genome. Behind the taxonomy for the genome you can find the '''contig''' the feature can be found on. The '''internal links''' you can see in the next row are leading to different pages containing other views and information for the feature. The [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] ('''genome browser''') displays the feature in the context of its genome. '''evidence''' leads to the [[SEED_Viewer_Manual/Evidence|Evidence]] page showing evidence for the annotation of the feature in form of [[Glossary/Similarities|Similarities]] and protein domains. Downloading the actual sequence for the feature is possible using the [[SEED_Viewer_Manual/ShowSeqs|Sequence Page]] ('''sequence''') link. Behind the external links you find a link to the '''ACH''' essentially identical genes. This link leads to the [[AnnotationClearingHouse|Annotation Clearing House]], a collection of proteins from many different sources. Proteins that have essentially the same sequence are grouped. For a given ID, you can see all IDs from different sources that belong to this group. At '''PubMed Links''' you can see the PubMed IDs to papers linked to the NCBI Entrez Database. The PubMed IDs shown are direct literature links attached directly to a feature, so-called '''dlits'''. '''FIGfams''' are protein families based on the subsystems technology. If you find an entry in this fields, the feature is part of the stated FIGfam. The link leads to the [[SEED_Viewer_Manual/FIGfams|FIGfam Viewer]]. '''database cross references''' link the feature to its entries (Aliases) in other databases like UniProt, GenBANK and many others. To gain more information about a feature, you can run different tools (e.g. PSI-BLAST, InterPro and many others) on your feature. Select a tool and press the button '''run tool'''. [[Image:AnnotationFeat.png]] === Reasons for Current Assignment === To gain a clue about what evidence an assignment of a functional role to your feature is based on, the text in '''Reasons for Current Assignment''' summarizes important information supporting the annotation. Additional to the information in the overview table, a list of indirect literature ('''ilits''') is decribed in the text. Those are based on direct literature to similar features that have the same functional role. [[Image:AnnotationAnnot.png]] === Compare Regions === The first line of the '''Compare Regions''' is a graphical display of the region of the feature its genome. All proteins are shown as colored arrows, where the direction depicts the strand of the feature. RNAs and other features are small boxes on the line. If two features overlap, the overlapping will be drawn on an (invisible) second line. The graph is centered on the selected feature (numbered 1), which is always colored red. Below you find the same region for orthologs in other (related) organisms, also colored in red. The colors of the other features (as well as the numbers) also represent ortholog (or sometimes also paralog) features. Whenever there are at least two ortholog or paralog features of a kind, a color (and a number) is assigned to them. '''Display Options''' are divided into two ''Regular'' and ''Advanced''. In the '''Regular''' options, you can change the ''Region Size'' and the ''Number of Regions''. Changing the '''Region Size''' enables to zoom in or out of the region. Changing the '''Number of Regions''' will add or remove genomes to your display. Click '''update graphics''' to change the display. The numbers that you put in for these values will be saved as [[SEED_Viewer_Manual/Preferences|preferences]]. [[Image:AnnotationComp.png]] If you click '''Advanced''' options, you will see the default options that are used for the Compare Regions View. The '''Pinned CDS Selection''' refers to the chosen peg and its orthologs in other genomes. The selection of genomes to show in the graphics can be made by ''Similarity'' or ''PCH pin''. The default is '''Similarity''' and means that the genomes are chosen using the similarity of the selected genes to its orthologs in other genomes. A '''PCH''' means a ''pair of close homologs''. [...] In the cell '''Genome Selection''' you can choose to ''collapse close genomes''. For many organism groups, the SEED database contains a number of strains that do not differ too strongly. They can be removed from the display using this option. The genomes in the display can be sorted by ''Phylogeny'' or ''Phylogenetic distance to input CDS''. In the first case, the genome of the selected peg may not appear on the first line any more, but the genomes in the display are sorted by the overall phylogeny. The second (default) options will show the selected peg's region on the first line and the other genomes in order of phylogenetic distance to the peg. [[Image:AnnotationAdv.png]] [[Image:AnnotationTabl.png]] 5b9e31fb20f2d4bc0c4f0a3ad83b529737ef9998 2006 2005 2008-11-24T12:28:44Z DanielaBartels 10 /* Compare Regions */ wikitext text/x-wiki == Annotation == The Annotation page shows a variaty of information about a single feature like a protein or an RNA. The page is roughly divided into three parts. The '''Annotation Overview''' presents the basic information about the feature. '''Reasons for Current Assignment''' reflect why the feature was assigned with the current functional role. The third part is a '''Compare Regions View''' showing the region of the feature in context to its own and related genomes. If you are logged in and the feature belongs to your private genome, this page will have additional options for you to annotate the feature. These are described [[SEED_Viewer_Manual/Editing_Capabilities/Annotation|here]]. === The Annotation Overview === The feature ID and the genome it belongs to are shown in the header line of this part of the page. They link to [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] and the [[SEED_Viewer_Manual/OrganismPage|Organism Page]], respectively. The '''current annotation''' depicts the functional role that is currently assigned to the feature. As annotations can be changed by users, you have the option to view an annotation history by pressing the '''show''' button in the cell '''annotation history''' some rows below. It will open a small table listing the date, the curator and the annotation that was made for each entry. As the genome name for the feature is already presented in the header of this section, we additionally show the '''taxonomy id''' for that genome in the overview. The link will lead to the Taxonomy Browser at the NCBI showing the taxonomy information for that genome. Behind the taxonomy for the genome you can find the '''contig''' the feature can be found on. The '''internal links''' you can see in the next row are leading to different pages containing other views and information for the feature. The [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] ('''genome browser''') displays the feature in the context of its genome. '''evidence''' leads to the [[SEED_Viewer_Manual/Evidence|Evidence]] page showing evidence for the annotation of the feature in form of [[Glossary/Similarities|Similarities]] and protein domains. Downloading the actual sequence for the feature is possible using the [[SEED_Viewer_Manual/ShowSeqs|Sequence Page]] ('''sequence''') link. Behind the external links you find a link to the '''ACH''' essentially identical genes. This link leads to the [[AnnotationClearingHouse|Annotation Clearing House]], a collection of proteins from many different sources. Proteins that have essentially the same sequence are grouped. For a given ID, you can see all IDs from different sources that belong to this group. At '''PubMed Links''' you can see the PubMed IDs to papers linked to the NCBI Entrez Database. The PubMed IDs shown are direct literature links attached directly to a feature, so-called '''dlits'''. '''FIGfams''' are protein families based on the subsystems technology. If you find an entry in this fields, the feature is part of the stated FIGfam. The link leads to the [[SEED_Viewer_Manual/FIGfams|FIGfam Viewer]]. '''database cross references''' link the feature to its entries (Aliases) in other databases like UniProt, GenBANK and many others. To gain more information about a feature, you can run different tools (e.g. PSI-BLAST, InterPro and many others) on your feature. Select a tool and press the button '''run tool'''. [[Image:AnnotationFeat.png]] === Reasons for Current Assignment === To gain a clue about what evidence an assignment of a functional role to your feature is based on, the text in '''Reasons for Current Assignment''' summarizes important information supporting the annotation. Additional to the information in the overview table, a list of indirect literature ('''ilits''') is decribed in the text. Those are based on direct literature to similar features that have the same functional role. [[Image:AnnotationAnnot.png]] === Compare Regions === The first line of the '''Compare Regions''' is a graphical display of the region of the feature its genome. All proteins are shown as colored arrows, where the direction depicts the strand of the feature. RNAs and other features are small boxes on the line. If two features overlap, the overlapping will be drawn on an (invisible) second line. The graph is centered on the selected feature (numbered 1), which is always colored red. Below you find the same region for orthologs in other (related) organisms, also colored in red. The colors of the other features (as well as the numbers) also represent ortholog (or sometimes also paralog) features. Whenever there are at least two ortholog or paralog features of a kind, a color (and a number) is assigned to them. '''Display Options''' are divided into two ''Regular'' and ''Advanced''. In the '''Regular''' options, you can change the ''Region Size'' and the ''Number of Regions''. Changing the '''Region Size''' enables to zoom in or out of the region. Changing the '''Number of Regions''' will add or remove genomes to your display. Click '''update graphics''' to change the display. The numbers that you put in for these values will be saved as [[SEED_Viewer_Manual/Preferences|preferences]]. [[Image:AnnotationComp.png]] If you click '''Advanced''' options, you will see the default options that are used for the Compare Regions View. The '''Pinned CDS Selection''' refers to the chosen peg and its orthologs in other genomes. The selection of genomes to show in the graphics can be made by ''Similarity'' or ''PCH pin''. The default is '''Similarity''' and means that the genomes are chosen using the similarity of the selected genes to its orthologs in other genomes. A '''PCH''' means a ''pair of close homologs''. [...] In the cell '''Genome Selection''' you can choose to ''collapse close genomes''. For many organism groups, the SEED database contains a number of strains that do not differ too strongly. They can be removed from the display using this option. The genomes in the display can be sorted by '''Phylogeny''' or '''Phylogenetic distance to input CDS'''. In the first case, the genome of the selected peg may not appear on the first line any more, but the genomes in the display are sorted by the overall phylogeny. The second (default) options will show the selected CDSs region on the first line and the other genomes in order of phylogenetic distance to the peg. The '''Evalue cutoff for selection of pinned CDSs''' depicts the minimum similarity CDSs may have to the selected CDS so that the it's region is displayed. [[Image:AnnotationAdv.png]] [[Image:AnnotationTabl.png]] e5111b522a8a7a95eb08f4fac3c7e6a1494b49c9 2007 2006 2008-11-24T13:53:46Z DanielaBartels 10 /* Compare Regions */ wikitext text/x-wiki == Annotation == The Annotation page shows a variaty of information about a single feature like a protein or an RNA. The page is roughly divided into three parts. The '''Annotation Overview''' presents the basic information about the feature. '''Reasons for Current Assignment''' reflect why the feature was assigned with the current functional role. The third part is a '''Compare Regions View''' showing the region of the feature in context to its own and related genomes. If you are logged in and the feature belongs to your private genome, this page will have additional options for you to annotate the feature. These are described [[SEED_Viewer_Manual/Editing_Capabilities/Annotation|here]]. === The Annotation Overview === The feature ID and the genome it belongs to are shown in the header line of this part of the page. They link to [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] and the [[SEED_Viewer_Manual/OrganismPage|Organism Page]], respectively. The '''current annotation''' depicts the functional role that is currently assigned to the feature. As annotations can be changed by users, you have the option to view an annotation history by pressing the '''show''' button in the cell '''annotation history''' some rows below. It will open a small table listing the date, the curator and the annotation that was made for each entry. As the genome name for the feature is already presented in the header of this section, we additionally show the '''taxonomy id''' for that genome in the overview. The link will lead to the Taxonomy Browser at the NCBI showing the taxonomy information for that genome. Behind the taxonomy for the genome you can find the '''contig''' the feature can be found on. The '''internal links''' you can see in the next row are leading to different pages containing other views and information for the feature. The [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] ('''genome browser''') displays the feature in the context of its genome. '''evidence''' leads to the [[SEED_Viewer_Manual/Evidence|Evidence]] page showing evidence for the annotation of the feature in form of [[Glossary/Similarities|Similarities]] and protein domains. Downloading the actual sequence for the feature is possible using the [[SEED_Viewer_Manual/ShowSeqs|Sequence Page]] ('''sequence''') link. Behind the external links you find a link to the '''ACH''' essentially identical genes. This link leads to the [[AnnotationClearingHouse|Annotation Clearing House]], a collection of proteins from many different sources. Proteins that have essentially the same sequence are grouped. For a given ID, you can see all IDs from different sources that belong to this group. At '''PubMed Links''' you can see the PubMed IDs to papers linked to the NCBI Entrez Database. The PubMed IDs shown are direct literature links attached directly to a feature, so-called '''dlits'''. '''FIGfams''' are protein families based on the subsystems technology. If you find an entry in this fields, the feature is part of the stated FIGfam. The link leads to the [[SEED_Viewer_Manual/FIGfams|FIGfam Viewer]]. '''database cross references''' link the feature to its entries (Aliases) in other databases like UniProt, GenBANK and many others. To gain more information about a feature, you can run different tools (e.g. PSI-BLAST, InterPro and many others) on your feature. Select a tool and press the button '''run tool'''. [[Image:AnnotationFeat.png]] === Reasons for Current Assignment === To gain a clue about what evidence an assignment of a functional role to your feature is based on, the text in '''Reasons for Current Assignment''' summarizes important information supporting the annotation. Additional to the information in the overview table, a list of indirect literature ('''ilits''') is decribed in the text. Those are based on direct literature to similar features that have the same functional role. [[Image:AnnotationAnnot.png]] === Compare Regions === The first line of the '''Compare Regions''' is a graphical display of the region of the feature its genome. All proteins are shown as colored arrows, where the direction depicts the strand of the feature. RNAs and other features are small boxes on the line. If two features overlap, the overlapping will be drawn on an (invisible) second line. The graph is centered on the selected feature (numbered 1), which is always colored red. Below you find the same region for orthologs in other (related) organisms, also colored in red. The colors of the other features (as well as the numbers) also represent ortholog (or sometimes also paralog) features. Whenever there are at least two ortholog or paralog features of a kind, a color (and a number) is assigned to them. '''Display Options''' are divided into two ''Regular'' and ''Advanced''. In the '''Regular''' options, you can change the ''Region Size'' and the ''Number of Regions''. Changing the '''Region Size''' enables to zoom in or out of the region. Changing the '''Number of Regions''' will add or remove genomes to your display. Click '''update graphics''' to change the display. The numbers that you put in for these values will be saved as [[SEED_Viewer_Manual/Preferences|preferences]]. [[Image:AnnotationComp.png]] If you click '''Advanced''' options, you will see the default options that are used for the Compare Regions View. The '''Pinned CDS Selection''' refers to the chosen peg and its orthologs in other genomes. The selection of genomes to show in the graphics can be made by ''Similarity'' or ''PCH pin''. The default is '''Similarity''' and means that the genomes are chosen using the similarity of the selected genes to its orthologs in other genomes. A '''PCH''' means a ''pair of close homologs''. [...] In the cell '''Genome Selection''' you can choose to ''collapse close genomes''. For many organism groups, the SEED database contains a number of strains that do not differ too strongly. They can be removed from the display using this option. The genomes in the display can be sorted by '''Phylogeny''' or '''Phylogenetic distance to input CDS'''. In the first case, the genome of the selected peg may not appear on the first line any more, but the genomes in the display are sorted by the overall phylogeny. The second (default) options will show the selected CDSs region on the first line and the other genomes in order of phylogenetic distance to the peg. The '''Evalue cutoff for selection of pinned CDSs''' depicts the minimum similarity CDSs may have to the selected CDS so that the its region is displayed. Defining if CDSs are orthologs or paralogs to a given CDS and therefore colored as such can be done using the '''Evalue cutoff for coloring CDS sets'''. We have implemented two different '''Coloring algorithms''' for the display. Default is a fast algorithm that might not always be absolutely accurate. You can choose a slower, but exact algorithm for coloring if you are unsure. [[Image:AnnotationAdv.png]] [[Image:AnnotationTabl.png]] 48993228ca64f58dfe353db0fe0bf7da04a42ddd 2008 2007 2008-11-24T14:08:22Z DanielaBartels 10 /* Compare Regions */ wikitext text/x-wiki == Annotation == The Annotation page shows a variaty of information about a single feature like a protein or an RNA. The page is roughly divided into three parts. The '''Annotation Overview''' presents the basic information about the feature. '''Reasons for Current Assignment''' reflect why the feature was assigned with the current functional role. The third part is a '''Compare Regions View''' showing the region of the feature in context to its own and related genomes. If you are logged in and the feature belongs to your private genome, this page will have additional options for you to annotate the feature. These are described [[SEED_Viewer_Manual/Editing_Capabilities/Annotation|here]]. === The Annotation Overview === The feature ID and the genome it belongs to are shown in the header line of this part of the page. They link to [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] and the [[SEED_Viewer_Manual/OrganismPage|Organism Page]], respectively. The '''current annotation''' depicts the functional role that is currently assigned to the feature. As annotations can be changed by users, you have the option to view an annotation history by pressing the '''show''' button in the cell '''annotation history''' some rows below. It will open a small table listing the date, the curator and the annotation that was made for each entry. As the genome name for the feature is already presented in the header of this section, we additionally show the '''taxonomy id''' for that genome in the overview. The link will lead to the Taxonomy Browser at the NCBI showing the taxonomy information for that genome. Behind the taxonomy for the genome you can find the '''contig''' the feature can be found on. The '''internal links''' you can see in the next row are leading to different pages containing other views and information for the feature. The [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] ('''genome browser''') displays the feature in the context of its genome. '''evidence''' leads to the [[SEED_Viewer_Manual/Evidence|Evidence]] page showing evidence for the annotation of the feature in form of [[Glossary/Similarities|Similarities]] and protein domains. Downloading the actual sequence for the feature is possible using the [[SEED_Viewer_Manual/ShowSeqs|Sequence Page]] ('''sequence''') link. Behind the external links you find a link to the '''ACH''' essentially identical genes. This link leads to the [[AnnotationClearingHouse|Annotation Clearing House]], a collection of proteins from many different sources. Proteins that have essentially the same sequence are grouped. For a given ID, you can see all IDs from different sources that belong to this group. At '''PubMed Links''' you can see the PubMed IDs to papers linked to the NCBI Entrez Database. The PubMed IDs shown are direct literature links attached directly to a feature, so-called '''dlits'''. '''FIGfams''' are protein families based on the subsystems technology. If you find an entry in this fields, the feature is part of the stated FIGfam. The link leads to the [[SEED_Viewer_Manual/FIGfams|FIGfam Viewer]]. '''database cross references''' link the feature to its entries (Aliases) in other databases like UniProt, GenBANK and many others. To gain more information about a feature, you can run different tools (e.g. PSI-BLAST, InterPro and many others) on your feature. Select a tool and press the button '''run tool'''. [[Image:AnnotationFeat.png]] === Reasons for Current Assignment === To gain a clue about what evidence an assignment of a functional role to your feature is based on, the text in '''Reasons for Current Assignment''' summarizes important information supporting the annotation. Additional to the information in the overview table, a list of indirect literature ('''ilits''') is decribed in the text. Those are based on direct literature to similar features that have the same functional role. [[Image:AnnotationAnnot.png]] === Compare Regions === The first line of the '''Compare Regions''' is a graphical display of the region of the feature its genome. All proteins are shown as colored arrows, where the direction depicts the strand of the feature. RNAs and other features are small boxes on the line. If two features overlap, the overlapping will be drawn on an (invisible) second line. The graph is centered on the selected feature (numbered 1), which is always colored red. Below you find the same region for orthologs in other (related) organisms, also colored in red. The colors of the other features (as well as the numbers) also represent ortholog (or sometimes also paralog) features. Whenever there are at least two ortholog or paralog features of a kind, a color (and a number) is assigned to them. '''Display Options''' are divided into two ''Regular'' and ''Advanced''. In the '''Regular''' options, you can change the ''Region Size'' and the ''Number of Regions''. Changing the '''Region Size''' enables to zoom in or out of the region. Changing the '''Number of Regions''' will add or remove genomes to your display. Click '''update graphics''' to change the display. The numbers that you put in for these values will be saved as [[SEED_Viewer_Manual/Preferences|preferences]]. [[Image:AnnotationComp.png]] If you click '''Advanced''' options, you will see the default options that are used for the Compare Regions View. The '''Pinned CDS Selection''' refers to the chosen peg and its orthologs in other genomes. The selection of genomes to show in the graphics can be made by ''Similarity'' or ''PCH pin''. The default is '''Similarity''' and means that the genomes are chosen using the similarity of the selected genes to its orthologs in other genomes. A '''PCH''' means a ''pair of close homologs''. [...] In the cell '''Genome Selection''' you can choose to ''collapse close genomes''. For many organism groups, the SEED database contains a number of strains that do not differ too strongly. They can be removed from the display using this option. The genomes in the display can be sorted by '''Phylogeny''' or '''Phylogenetic distance to input CDS'''. In the first case, the genome of the selected peg may not appear on the first line any more, but the genomes in the display are sorted by the overall phylogeny. The second (default) options will show the selected CDSs region on the first line and the other genomes in order of phylogenetic distance to the peg. The '''Evalue cutoff for selection of pinned CDSs''' depicts the minimum similarity CDSs may have to the selected CDS so that the its region is displayed. Defining if CDSs are orthologs or paralogs to a given CDS and therefore colored as such can be done using the '''Evalue cutoff for coloring CDS sets'''. We have implemented two different '''Coloring algorithms''' for the display. Default is a fast algorithm that might not always be absolutely accurate. You can choose a slower, but exact algorithm for coloring if you are unsure. [[Image:AnnotationAdv.png]] The second tab of the Compare Regions tab view lists all visible features in a table, sorted by the genome they appear in. The entries in the '''ID''' column link to the Annotation page of the feature. Additional to Start, Stop, Strand and Functional Role of the feature, you can see a column ''FC'', an ''SS'', a ''Set'' and a ''CL''. '''FC''' stands for ''[[Glossary#Functional Coupling|Functionally coupled]]]'', showing the number of feature that are coupled to this feature via clustering genomes or other evidence. The '''SS''' column shows the subsystems the feature is in. '''Set''' is the number that is depicted above a colored feature in the graphic. The '''cluster''' buttons in the last column leads to the [[SEED_Viewer_Manual/HomologClusters|Homolog clusters]] [[Image:AnnotationTabl.png]] 1c707f83f1cd72eefa1ffec2b34a4cf72946d47c 2009 2008 2008-11-24T14:08:56Z DanielaBartels 10 /* Compare Regions */ wikitext text/x-wiki == Annotation == The Annotation page shows a variaty of information about a single feature like a protein or an RNA. The page is roughly divided into three parts. The '''Annotation Overview''' presents the basic information about the feature. '''Reasons for Current Assignment''' reflect why the feature was assigned with the current functional role. The third part is a '''Compare Regions View''' showing the region of the feature in context to its own and related genomes. If you are logged in and the feature belongs to your private genome, this page will have additional options for you to annotate the feature. These are described [[SEED_Viewer_Manual/Editing_Capabilities/Annotation|here]]. === The Annotation Overview === The feature ID and the genome it belongs to are shown in the header line of this part of the page. They link to [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] and the [[SEED_Viewer_Manual/OrganismPage|Organism Page]], respectively. The '''current annotation''' depicts the functional role that is currently assigned to the feature. As annotations can be changed by users, you have the option to view an annotation history by pressing the '''show''' button in the cell '''annotation history''' some rows below. It will open a small table listing the date, the curator and the annotation that was made for each entry. As the genome name for the feature is already presented in the header of this section, we additionally show the '''taxonomy id''' for that genome in the overview. The link will lead to the Taxonomy Browser at the NCBI showing the taxonomy information for that genome. Behind the taxonomy for the genome you can find the '''contig''' the feature can be found on. The '''internal links''' you can see in the next row are leading to different pages containing other views and information for the feature. The [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] ('''genome browser''') displays the feature in the context of its genome. '''evidence''' leads to the [[SEED_Viewer_Manual/Evidence|Evidence]] page showing evidence for the annotation of the feature in form of [[Glossary/Similarities|Similarities]] and protein domains. Downloading the actual sequence for the feature is possible using the [[SEED_Viewer_Manual/ShowSeqs|Sequence Page]] ('''sequence''') link. Behind the external links you find a link to the '''ACH''' essentially identical genes. This link leads to the [[AnnotationClearingHouse|Annotation Clearing House]], a collection of proteins from many different sources. Proteins that have essentially the same sequence are grouped. For a given ID, you can see all IDs from different sources that belong to this group. At '''PubMed Links''' you can see the PubMed IDs to papers linked to the NCBI Entrez Database. The PubMed IDs shown are direct literature links attached directly to a feature, so-called '''dlits'''. '''FIGfams''' are protein families based on the subsystems technology. If you find an entry in this fields, the feature is part of the stated FIGfam. The link leads to the [[SEED_Viewer_Manual/FIGfams|FIGfam Viewer]]. '''database cross references''' link the feature to its entries (Aliases) in other databases like UniProt, GenBANK and many others. To gain more information about a feature, you can run different tools (e.g. PSI-BLAST, InterPro and many others) on your feature. Select a tool and press the button '''run tool'''. [[Image:AnnotationFeat.png]] === Reasons for Current Assignment === To gain a clue about what evidence an assignment of a functional role to your feature is based on, the text in '''Reasons for Current Assignment''' summarizes important information supporting the annotation. Additional to the information in the overview table, a list of indirect literature ('''ilits''') is decribed in the text. Those are based on direct literature to similar features that have the same functional role. [[Image:AnnotationAnnot.png]] === Compare Regions === The first line of the '''Compare Regions''' is a graphical display of the region of the feature its genome. All proteins are shown as colored arrows, where the direction depicts the strand of the feature. RNAs and other features are small boxes on the line. If two features overlap, the overlapping will be drawn on an (invisible) second line. The graph is centered on the selected feature (numbered 1), which is always colored red. Below you find the same region for orthologs in other (related) organisms, also colored in red. The colors of the other features (as well as the numbers) also represent ortholog (or sometimes also paralog) features. Whenever there are at least two ortholog or paralog features of a kind, a color (and a number) is assigned to them. '''Display Options''' are divided into two ''Regular'' and ''Advanced''. In the '''Regular''' options, you can change the ''Region Size'' and the ''Number of Regions''. Changing the '''Region Size''' enables to zoom in or out of the region. Changing the '''Number of Regions''' will add or remove genomes to your display. Click '''update graphics''' to change the display. The numbers that you put in for these values will be saved as [[SEED_Viewer_Manual/Preferences|preferences]]. [[Image:AnnotationComp.png]] If you click '''Advanced''' options, you will see the default options that are used for the Compare Regions View. The '''Pinned CDS Selection''' refers to the chosen peg and its orthologs in other genomes. The selection of genomes to show in the graphics can be made by ''Similarity'' or ''PCH pin''. The default is '''Similarity''' and means that the genomes are chosen using the similarity of the selected genes to its orthologs in other genomes. A '''PCH''' means a ''pair of close homologs''. [...] In the cell '''Genome Selection''' you can choose to ''collapse close genomes''. For many organism groups, the SEED database contains a number of strains that do not differ too strongly. They can be removed from the display using this option. The genomes in the display can be sorted by '''Phylogeny''' or '''Phylogenetic distance to input CDS'''. In the first case, the genome of the selected peg may not appear on the first line any more, but the genomes in the display are sorted by the overall phylogeny. The second (default) options will show the selected CDSs region on the first line and the other genomes in order of phylogenetic distance to the peg. The '''Evalue cutoff for selection of pinned CDSs''' depicts the minimum similarity CDSs may have to the selected CDS so that the its region is displayed. Defining if CDSs are orthologs or paralogs to a given CDS and therefore colored as such can be done using the '''Evalue cutoff for coloring CDS sets'''. We have implemented two different '''Coloring algorithms''' for the display. Default is a fast algorithm that might not always be absolutely accurate. You can choose a slower, but exact algorithm for coloring if you are unsure. [[Image:AnnotationAdv.png]] The second tab of the Compare Regions tab view lists all visible features in a table, sorted by the genome they appear in. The entries in the '''ID''' column link to the Annotation page of the feature. Additional to Start, Stop, Strand and Functional Role of the feature, you can see a column ''FC'', an ''SS'', a ''Set'' and a ''CL''. '''FC''' stands for ''[[Glossary#Functional Coupling|Functionally coupled]]'', showing the number of feature that are coupled to this feature via clustering genomes or other evidence. The '''SS''' column shows the subsystems the feature is in. '''Set''' is the number that is depicted above a colored feature in the graphic. The '''cluster''' buttons in the last column leads to the [[SEED_Viewer_Manual/HomologClusters|Homolog clusters]] [[Image:AnnotationTabl.png]] fa1d505a87fbfc2c483f86997c25efbd7f68a6c4 2010 2009 2008-11-24T14:09:34Z DanielaBartels 10 /* Compare Regions */ wikitext text/x-wiki == Annotation == The Annotation page shows a variaty of information about a single feature like a protein or an RNA. The page is roughly divided into three parts. The '''Annotation Overview''' presents the basic information about the feature. '''Reasons for Current Assignment''' reflect why the feature was assigned with the current functional role. The third part is a '''Compare Regions View''' showing the region of the feature in context to its own and related genomes. If you are logged in and the feature belongs to your private genome, this page will have additional options for you to annotate the feature. These are described [[SEED_Viewer_Manual/Editing_Capabilities/Annotation|here]]. === The Annotation Overview === The feature ID and the genome it belongs to are shown in the header line of this part of the page. They link to [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] and the [[SEED_Viewer_Manual/OrganismPage|Organism Page]], respectively. The '''current annotation''' depicts the functional role that is currently assigned to the feature. As annotations can be changed by users, you have the option to view an annotation history by pressing the '''show''' button in the cell '''annotation history''' some rows below. It will open a small table listing the date, the curator and the annotation that was made for each entry. As the genome name for the feature is already presented in the header of this section, we additionally show the '''taxonomy id''' for that genome in the overview. The link will lead to the Taxonomy Browser at the NCBI showing the taxonomy information for that genome. Behind the taxonomy for the genome you can find the '''contig''' the feature can be found on. The '''internal links''' you can see in the next row are leading to different pages containing other views and information for the feature. The [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] ('''genome browser''') displays the feature in the context of its genome. '''evidence''' leads to the [[SEED_Viewer_Manual/Evidence|Evidence]] page showing evidence for the annotation of the feature in form of [[Glossary/Similarities|Similarities]] and protein domains. Downloading the actual sequence for the feature is possible using the [[SEED_Viewer_Manual/ShowSeqs|Sequence Page]] ('''sequence''') link. Behind the external links you find a link to the '''ACH''' essentially identical genes. This link leads to the [[AnnotationClearingHouse|Annotation Clearing House]], a collection of proteins from many different sources. Proteins that have essentially the same sequence are grouped. For a given ID, you can see all IDs from different sources that belong to this group. At '''PubMed Links''' you can see the PubMed IDs to papers linked to the NCBI Entrez Database. The PubMed IDs shown are direct literature links attached directly to a feature, so-called '''dlits'''. '''FIGfams''' are protein families based on the subsystems technology. If you find an entry in this fields, the feature is part of the stated FIGfam. The link leads to the [[SEED_Viewer_Manual/FIGfams|FIGfam Viewer]]. '''database cross references''' link the feature to its entries (Aliases) in other databases like UniProt, GenBANK and many others. To gain more information about a feature, you can run different tools (e.g. PSI-BLAST, InterPro and many others) on your feature. Select a tool and press the button '''run tool'''. [[Image:AnnotationFeat.png]] === Reasons for Current Assignment === To gain a clue about what evidence an assignment of a functional role to your feature is based on, the text in '''Reasons for Current Assignment''' summarizes important information supporting the annotation. Additional to the information in the overview table, a list of indirect literature ('''ilits''') is decribed in the text. Those are based on direct literature to similar features that have the same functional role. [[Image:AnnotationAnnot.png]] === Compare Regions === The first line of the '''Compare Regions''' is a graphical display of the region of the feature its genome. All proteins are shown as colored arrows, where the direction depicts the strand of the feature. RNAs and other features are small boxes on the line. If two features overlap, the overlapping will be drawn on an (invisible) second line. The graph is centered on the selected feature (numbered 1), which is always colored red. Below you find the same region for orthologs in other (related) organisms, also colored in red. The colors of the other features (as well as the numbers) also represent ortholog (or sometimes also paralog) features. Whenever there are at least two ortholog or paralog features of a kind, a color (and a number) is assigned to them. '''Display Options''' are divided into two ''Regular'' and ''Advanced''. In the '''Regular''' options, you can change the ''Region Size'' and the ''Number of Regions''. Changing the '''Region Size''' enables to zoom in or out of the region. Changing the '''Number of Regions''' will add or remove genomes to your display. Click '''update graphics''' to change the display. The numbers that you put in for these values will be saved as [[SEED_Viewer_Manual/Preferences|preferences]]. [[Image:AnnotationComp.png]] If you click '''Advanced''' options, you will see the default options that are used for the Compare Regions View. The '''Pinned CDS Selection''' refers to the chosen peg and its orthologs in other genomes. The selection of genomes to show in the graphics can be made by ''Similarity'' or ''PCH pin''. The default is '''Similarity''' and means that the genomes are chosen using the similarity of the selected genes to its orthologs in other genomes. A '''PCH''' means a ''pair of close homologs''. [...] In the cell '''Genome Selection''' you can choose to ''collapse close genomes''. For many organism groups, the SEED database contains a number of strains that do not differ too strongly. They can be removed from the display using this option. The genomes in the display can be sorted by '''Phylogeny''' or '''Phylogenetic distance to input CDS'''. In the first case, the genome of the selected peg may not appear on the first line any more, but the genomes in the display are sorted by the overall phylogeny. The second (default) options will show the selected CDSs region on the first line and the other genomes in order of phylogenetic distance to the peg. The '''Evalue cutoff for selection of pinned CDSs''' depicts the minimum similarity CDSs may have to the selected CDS so that the its region is displayed. Defining if CDSs are orthologs or paralogs to a given CDS and therefore colored as such can be done using the '''Evalue cutoff for coloring CDS sets'''. We have implemented two different '''Coloring algorithms''' for the display. Default is a fast algorithm that might not always be absolutely accurate. You can choose a slower, but exact algorithm for coloring if you are unsure. [[Image:AnnotationAdv.png]] The second tab of the Compare Regions tab view lists all visible features in a table, sorted by the genome they appear in. The entries in the '''ID''' column link to the Annotation page of the feature. Additional to Start, Stop, Strand and Functional Role of the feature, you can see a column ''FC'', an ''SS'', a ''Set'' and a ''CL''. '''FC''' stands for ''[[Glossary#Functional Coupling|Functionally coupled]]'', showing the number of feature that are coupled to this feature via clustering genomes or other evidence. The '''SS''' column shows the subsystems the feature is in. '''Set''' is the number that is depicted above a colored feature in the graphic. The '''cluster''' buttons in the last column leads to the [[SEED_Viewer_Manual/HomologClusters|Homolog clusters]] page for that feature. [[Image:AnnotationTabl.png]] 4c0723220ed6614b525586a1be958c5640cdb71f 6 1498 1998 2008-11-24T11:29:49Z DanielaBartels 10 wikitext text/x-wiki da39a3ee5e6b4b0d3255bfef95601890afd80709 6 1499 2002 2008-11-24T11:43:16Z DanielaBartels 10 wikitext text/x-wiki da39a3ee5e6b4b0d3255bfef95601890afd80709 0 1500 2011 2008-11-24T14:20:36Z DanielaBartels 10 wikitext text/x-wiki Genes who's relative position is conserved in at least four other species are functionally coupled 6615bbcd32ba7656688b6bc69da752870955a1fb 2012 2011 2008-11-24T14:24:09Z DanielaBartels 10 wikitext text/x-wiki == Homolog cluster == # returns the homolog cluster table, where 'homology' is inferred by similarity score. # For a given organism, only pegs which are in clusters are considered, and only # a single peg (the one with the best sim score) is reported. evalue: 1.0e-10 maximal 50 homolog features Genes who's relative position is conserved in at least four other species are functionally coupled ddf0e8b953d4fa75604e54abedb3befd24f8cf55 2014 2012 2008-11-24T14:34:27Z DanielaBartels 10 /* Homolog cluster */ wikitext text/x-wiki == Homolog cluster == # returns the homolog cluster table, where 'homology' is inferred by similarity score. # For a given organism, only pegs which are in clusters are considered, and only # a single peg (the one with the best sim score) is reported. evalue: 1.0e-10 maximal 50 homolog features Genes who's relative position is conserved in at least four other species are functionally coupled [[Image:HomologClusters.png]] 6edd803c6b24f4dbdf59d47e59c58755b315ebf1 2016 2014 2008-11-24T14:46:08Z DanielaBartels 10 /* Homolog cluster */ wikitext text/x-wiki == Homolog cluster == This page shows the homolog cluster table for a given feature, where ''homology'' is inferred by similarity score. The ''cluster'' is computed using [[Glossary#Functional Coupling|Functional coupling]] as a basis. For a given organism, only features which are in clusters are considered, and only a single feature (the one with the best similarity score) is reported. The table consists of maximal 50 homolog features, and the evalue cutoff is e -10. On the top of the page a small table shows some information about the query feature. The '''Input Feature ID''' links to the [[SEED_Viewer_Manual/Annotation|Annotation Page]] for the feature. The '''Organism''' link leads to the respective [[SEED_Viewer_Manual/OrganismPage|Organism Page]]. The '''Cluster Size''' depicts how many features in that organism belong to the computed cluster. The '''Function''' of the query peg is depicted next, as well as '''Other functions in the cluster''', meaning the functions of the other features in that genome that are computed to belong to the cluster. [[Image:HomologClusters.png]] 70876429ce511759e481cf3eb14670db29e26d2b 2017 2016 2008-11-24T14:46:31Z DanielaBartels 10 /* Homolog cluster */ wikitext text/x-wiki == Homolog cluster == This page shows the homolog cluster table for a given feature, where ''homology'' is inferred by similarity score. The ''cluster'' is computed using [[Glossary#Functional coupling|Functional coupling]] as a basis. For a given organism, only features which are in clusters are considered, and only a single feature (the one with the best similarity score) is reported. The table consists of maximal 50 homolog features, and the evalue cutoff is e -10. On the top of the page a small table shows some information about the query feature. The '''Input Feature ID''' links to the [[SEED_Viewer_Manual/Annotation|Annotation Page]] for the feature. The '''Organism''' link leads to the respective [[SEED_Viewer_Manual/OrganismPage|Organism Page]]. The '''Cluster Size''' depicts how many features in that organism belong to the computed cluster. The '''Function''' of the query peg is depicted next, as well as '''Other functions in the cluster''', meaning the functions of the other features in that genome that are computed to belong to the cluster. [[Image:HomologClusters.png]] a7392a56addc8b1e00319548aba7300ef8b2edd1 2018 2017 2008-11-24T14:48:45Z DanielaBartels 10 /* Homolog cluster */ wikitext text/x-wiki == Homolog cluster == This page shows the homolog cluster table for a given feature, where ''homology'' is inferred by similarity score. The ''cluster'' is computed using [[Glossary#Functional coupling|Functional coupling]] as a basis. For a given organism, only features which are in clusters are considered, and only a single feature (the one with the best similarity score) is reported. The table consists of maximal 50 homolog features, and the evalue cutoff is e -10. On the top of the page a small table shows some information about the query feature. The '''Input Feature ID''' links to the [[SEED_Viewer_Manual/Annotation|Annotation Page]] for the feature. The '''Organism''' link leads to the respective [[SEED_Viewer_Manual/OrganismPage|Organism Page]]. The '''Cluster Size''' depicts how many features in that organism belong to the computed cluster. The '''Function''' of the query peg is depicted next, as well as '''Other functions in the cluster''', meaning the functions of the other features in that genome that are computed to belong to the cluster. The following table of all features in the computed homolog cluster shows you the same information for each feature, as well as Aliases for that features in other databases. [[Image:HomologClusters.png]] a90c8e966a132e35c9a72948709d5eabc058942c 2019 2018 2008-11-24T14:49:11Z DanielaBartels 10 /* Homolog cluster */ wikitext text/x-wiki == Homolog cluster == This page shows the homolog cluster table for a given feature, where ''homology'' is inferred by similarity score. The ''cluster'' is computed using [[Glossary#Functional coupling|Functional coupling]] as a basis. For a given organism, only features which are in clusters are considered, and only a single feature (the one with the best similarity score) is reported. The table consists of maximal 50 homolog features, and the evalue cutoff is e -10. On the top of the page a small table shows some information about the query feature. The '''Input Feature ID''' links to the [[SEED_Viewer_Manual/Annotation|Annotation Page]] for the feature. The '''Organism''' link leads to the respective [[SEED_Viewer_Manual/OrganismPage|Organism Page]]. The '''Cluster Size''' depicts how many features in that organism belong to the computed cluster. The '''Function''' of the query peg is depicted next, as well as '''Other functions in the cluster''', meaning the functions of the other features in that genome that are computed to belong to the cluster. The following table of all features in the computed homolog cluster shows you the same information for each feature, as well as '''Aliases''' for that features in other databases. [[Image:HomologClusters.png]] 6883ef5b3bc235db5ee20d71bee2354783cae0f0 2020 2019 2008-11-24T15:05:12Z DanielaBartels 10 /* Homolog cluster */ wikitext text/x-wiki == Homolog cluster == This page shows the homolog cluster table for a given feature, where ''homology'' is inferred by similarity score. The ''cluster'' is computed using [[Glossary#Functional coupling|Functional coupling]] as a basis. For a given organism, only features which are in clusters are considered, and only a single feature (the one with the best similarity score) is reported. The table consists of maximal 50 homolog features, and the evalue cutoff is e -10. On the top of the page a small table shows some information about the query feature. The '''Input Feature ID''' links to the [[SEED_Viewer_Manual/Annotation|Annotation Page]] for the feature. The '''Organism''' link leads to the respective [[SEED_Viewer_Manual/OrganismPage|Organism Page]]. The '''Cluster Size''' depicts how many features in that organism belong to the computed cluster. The '''Function''' of the query peg is depicted next, as well as '''Other functions in the cluster''', meaning the functions of the other features in that genome that are computed to belong to the cluster. The following table of all features in the computed homolog cluster shows you the same information for each feature, as well as '''Aliases''' for that features in other databases. The column '''Cluster Functions''' includes the functions of the stated feature, which is marked in red. [[Image:HomologClusters.png]] 6ee40ff1779a59c5f6cabb3bc03c04e79344f145 0 1367 2013 1757 2008-11-24T14:32:23Z DanielaBartels 10 wikitext text/x-wiki === Annotators SEED === The master copy for all data in the SEED environment. Users can not access this password protected site. All annotations are made available via the [[#SEED-Viewer| SEED-Viewer]] and the [[#Trial-SEED|Trial-SEED]]. === Annotation === please see [[#Assigning_a_gene_function_and_annotation| Assigning a gene function and annotation]] === Assigning a gene function and annotation === Annotators assign gene functions to genes, and we call this process annotation. In most contexts, people use the term annotation to refer to assignments of function to the genes within a single organism. We certainly use the term in this sense, but we also use it to describe the process of assigning functions to corresponding genes from numerous genomes. Our basic approach to annotation is to ask our annotators to annotate the genes included in a [[#subsystem|Subsystem]] (e.g., glycolysis) across all genomes. This process of annotation of the genes within a subsystem across a set of genomes, rather than annotation of genes within a single genome, allows our annotators to focus on a constrained set of functional roles and attempt to accurately identify exactly what variant, if any, of a subsystem exists in each of the genomes. We use the term annotation to refer to assigning functions to genes (either within a single organism or to a constrained set of gene/protein families across a set of organisms). This activity certainly is closely related to the construction of subsystems and protein families (which we call FIGfams), but we will describe those activities elsewhere. === Assignment === please see [[#Assigning_a_gene_function_and_annotation| Assigning a gene function and annotation]] === Bidirectional Best Hit (BBH) === The paper [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=EBI&pubmedid=10077608 The use of gene clusters to infer functional coupling] defines a Bidirectional Best Hit or BBH as follows: <blockquote> Given two genes Xa and Xb from two genomes Ga and Gb, Xa and Xb are called a “bidirectional best hit (BBH)” if and only if recognizable similarity exists between them (in our case, we required fasta3 scores lower than 1.0 × 10−5), there is no gene Zb in Gb that is more similar than Xb is to Xa, and there is no gene Za in Ga that is more similar than Xa is to Xb. Genes (Xa, Ya) from Ga and (Xb, Yb) from Gb form a “pair of close bidirectional best hits (PCBBH)” if and only if Xa and Ya are close, Xb and Yb are close, Xa and Xb are a BBH, and Ya and Yb are a BBH. </blockquote> === Clearinghouse === please see [[#SubsystemClearinghouse|Subsystem Clearinghouse]] ===Feature=== A feature is a defined region in the DNA. A PEG is the most prevalent feature type in the SEED. Some other feature types include RNA, prophage and pathogenicity islands. The format for a feature ID is fig|genome_id.feature_abbreviation.feature_number (ie fig|83333.1.peg.100 ). === FIGfam === FIGfams are protein families generated by the Fellowship for Interpretation of Genomes (FIG). These families are based on the collection of subsystems, as well as correspondences between genes in closely related strains (we describe the construction of FIGfams in a separate SOP). The important properties of these families are as follows: # Two PEGs which both occur within a single FIGfam are believed to have the same function. # There is a decision procedure associated with the family which can be invoked to determine whether or not a gene can be “safely” assigned the function associated with the family. === FIG Identifier / FIG-IDs === We provide identifiers for genome sequences and features in the following form: {| ! Entity type !! key !! identifier |- | Genome || genome || fig<nowiki>|</nowiki>83331.1 |- | PEG || id || fig<nowiki>|</nowiki>83331.peg.123 |- | RNA feature || id || fig<nowiki>|</nowiki>83331.rna.1 |- |} (Please also see below for information on how to link to the SEED.) === Functional coupling === The availability of multiple genomes provides an opportunity to gain new insights into the processes that drive the dispersion and formation of chromosomal gene clusters. The paper [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=EBI&pubmedid=10077608 The use of gene clusters to infer functional coupling] describes a method to compute functional coupling of features due to conserved gene clusters . === Functional role === The concept of functional role is both basic and primitive in the sense that we will not pretend to offer a precise definition. It corresponds roughly to a single logical role that a gene or gene product may play in the operation of a cell. === Gene function === The function of a protein-encoding gene (PEG) is the functional role played by the product of the gene or an expression describing a set of roles played by the encoded protein. The operators used to construct expressions and the meanings associated with the operators are described in http://www.nmpdr.org/FIG/Html/SEED_functions.html Genes other than PEGs can also be assigned functions (e.g., SSU rRNA). However, in most cases the functions assigned to genes other than PEGs tend not to be problematic. === Linking to the SEED === We support linking to the SEED using a generic mechanism: Base URL: http://www.theseed.org/linkin.cgi? {| |+ Supported SEED Identifiers for external use ! Entity type !! key !! identifier !! Example |- | Genome || genome || fig<nowiki>|</nowiki>83331.1 || [[http://www.theseed.org/linkin.cgi?genome=fig|83333.1 http://www.theseed.org/linkin.cgi?genome=fig&#124;83333.1]] |- | PEG || id || fig<nowiki>|</nowiki>83331.peg.123 || [[http://www.theseed.org/linkin.cgi?id=fig|83333.1.peg.123 http://www.theseed.org/linkin.cgi?id=fig&#124;83333.1.peg.123]] |- | RNA feature || id || fig<nowiki>|</nowiki>83331.rna.1 || [[http://www.theseed.org/linkin.cgi?id=fig|83333.1.rna.1 http://www.theseed.org/linkin.cgi?id=fig&#124;83333.1.rna.1]] |- |} SEED identifiers contain the NCBI taxonomy ID, thus if the taxonomy ID changes, we need to update our internal data accordingly. To provide stable external identifiers, we keep a list of IDs that have changed and display warning message informing the user of the change and provide a link to the new version of the data requested. === Metabolic Reconstruction === When we use the term metabolic reconstruction of a given genome we will simply mean the set of populated subsystems that contain the genome, the PEGs (and their assigned functions) that are connected to functional roles in these populated subsystems, and the specific variant code associated with the genome in each of the populated subsystems. === NMPDR pathogen genome === The NMPDR is responsible for five classes of genomes: # Campylobacter jejuni # Listeria monocytogenes # Staphylococcus aureus # Streptococcus pneumoniae and Streptococcus pyogenes # Pathogenic Vibrio === Pair of Close Homologs (PCH) === The paper [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=EBI&pubmedid=10077608 The use of gene clusters to infer functional coupling] defines a Pair of Close Homologs as follows: <blockquote> We can also define the concept of “pairs of close homologs” (PCHs) as follows: genes (X′a, Y′a) from Ga and (X′b, Y′b) from Gb form a PCH if and only if X′a and Y′a are close, X′b and Y′b are close, X′a and X′b are recognizably similar, and Y′a and Y′b are recognizably similar. Here, we will consider two genes to be recognizably similar if their gene products produce fasta3 scores lower than 1.0 × 10−5. We use a scoring scheme analogous to the one described for PCBBHs to evaluate the connections between PCHs, except that if Ga and Gb are the same genome, we assign an arbitrary “same-genome score” (“same-genome” pairs cannot occur for PCBBHs by definition, but for PCHs they are possible). Unlike PCBBHs from two very close genomes for which contiguity is completely uninformative in the vast majority of cases, PCHs allow recognition of gene clusters that play similar (but usually not identical) roles (such as two transport cassettes containing pairs of homologs) in the same or similar organisms. The arbitrary “same-genome score” should, we believe, have a value that is high enough to rank such instances as significant. </blockquote> === PEG === A Protein Encoding Gene (PEG) is equivalent to a CDS (Coding Sequence). === Populated Subsystem === please see [[#Subsystem|Subsystem]] === RAST === RAST or Rapid Annotation using Subsystem Technology is a rapid and very accurate annotation technology. We make a RAST server available for public use at http://rast.nmpdr.org === SEED-Viewer === The SEED Viewer is a web-based application that allows browsing of SEED data structures. We use the SEED-Viewer to provide a public read-only version of the latest SEED data at: http://seed-viewer.theseed.org '''Please note''': The data is updated automatically every 24 hours. When citing or linking to the SEED please use this version. === Subsystem === A subsystem is a set of functional roles that an annotator has decided should be thought of as related. Frequently, subsystems represent the collection of [[#Functional_role|functional roles]] that make up a metabolic pathway, a complex (e.g., the ribosome), or a class of proteins (e.g., two-component signal-transduction proteins within Staphylococcus aureus). A '''populated subsystem''' is a subsystem with an attached spreadsheet. The rows of the spreadsheet represent genomes and the columns represent the functional roles of the spreadsheet. Each cell contains the identifiers of genes from the corresponding genome the implement the specific functional role. That is, a populated subsystem specifies which genes implement instances of the subsystem in each of the genomes. The rows of a populated genome are assigned '''variant codes''' which describe which of a set of possible variants of the subsystem exist within each genome (special codes expressing a total absence of the subsystem or remaining uncertainty exist). Construction of a large set of curated populated subsystems is at the center of the NMPDR and SEED annotation efforts. === Subsystem Clearing House === Since annotators can work on any machine (including the public SEED) the way to propagate subsystems is via http://clearinghouse.theseed.org/clearinghouse_browser.cgi? === Trial-SEED === A public, read-write copy of the SEED is made available on http://theseed.uchicago.edu/FIG/index.cgi '''Please note''': The data on this server is updated in irregular intervals. Users should not assume that annotations made on this system will persist. Please publish your annotations to the [[#Subsystem_clearing_house|Subsystem Clearing house]]. === Variant Code=== please see [[#Subsystem|Subsystem]] 2c5ad42019a4573f397655486e9ee55b6f792cd2 6 1501 2015 2008-11-24T14:34:44Z DanielaBartels 10 wikitext text/x-wiki da39a3ee5e6b4b0d3255bfef95601890afd80709 0 1466 2021 1972 2008-11-24T15:08:14Z DanielaBartels 10 /* Main pages of the SeedViewer */ wikitext text/x-wiki == Main pages of the SeedViewer == ''' [[SEED_Viewer_Manual|Home Page]] ''' ''' [[SEED_Viewer_Manual|Menu]] ''' === Subsystem Select === === Subsystems === === Functional Role === === FigFams === '''[[SEED_Viewer_Manual/Annotation|Annotation]]''' === Evidence === '''[[SEED_Viewer_Manual/BLASTOrganism|BLAST against an organism]]''' === Sequence === '''[[SEED_Viewer_Manual/GenomeBrowser|Browse Genome]]''' '''[[SEED_Viewer_Manual/OrganismSelect|Organism Select]]''' '''[[SEED_Viewer_Manual/OrganismPage|Organism Page]]''' === Kegg === '''[[SEED_Viewer_Manual/HomologClusters|Homolog Clusters]]''' c6a4129e35d4ba31e7480c3443037f0e8d8dd5d0 0 1502 2022 2008-11-24T15:23:59Z DanielaBartels 10 wikitext text/x-wiki The Evidence Page is divided into two parts via a [[WebComponents/Tabview|TabView]]: The '''Visual Protein Evidence''' and the '''Tabular Protein Evidence'''. == Visual Protein Evidence == === Location === === Domains === === Similarities === == Tabular Protein Evidence == === Similarities === === Domains === === Identical Proteins === === Functionally Coupled === 444a0f7191159babb8fc4995ecd243788303ed51 6 1503 2023 2008-11-24T15:35:53Z DanielaBartels 10 wikitext text/x-wiki da39a3ee5e6b4b0d3255bfef95601890afd80709 0 1478 2024 1934 2008-11-24T15:37:42Z DanielaBartels 10 /* FIGfams Menu */ wikitext text/x-wiki == Menu Overview == === Navigate Menu === This menu is present on every SeedViewer page. The first entry '''Startpage''' will lead to the SeedViewer [[SEED_Viewer_Manual|HomePage]]. '''Organisms''' will open the [[SEED_Viewer_Manual/OrganismSelect|Organism Select]] page. You will see an overview of all organisms in the SEED and are able to select one to view in detail. '''Subsystems''' will do the same for subsystems. '''FIGFams''' leads to an entry point for browsing [[SEED_Viewer_Manual/FIGfams|FIGfams]]. You can find more information about FIGfams [[Glossary#FIGfam|here]]. The '''BLAST Search''' links to the [[SEED_Viewer_Manual/BLASTOrganism|BLAST Page]]. You will be able to BLAST a sequence against an organism in the SEED. [[Image:MenuNav.png]] === Help Menu === This menu is also present on all SeedViewer pages. The first link '''What is the SEED''' will lead you to the [[Home_of_the_SEED|SEED Homepage]]. Clicking the second link '''How to use the SEED Viewer''' will get you to this wiki. '''Submitting data to SEED''' lets you browse the [[RAST_Tutorial|RAST Tutorial]]. '''Contact''' enables you to write an email to the SEED team. Clicking '''Register''' is the first step to get a user account. It will lead to the [[SEED_Viewer_Manual/Register|Register]] page. '''I forgot my password''' enables you to [[SEED_Viewer_Manual/RequestNewPassword|Request a new password]]. [[Image:MenuHelp.png]] === Organism Menu === In the context of a selected organism, an organism menu will appear. '''General Information''' will lead to the [[SEED_Viewer_Manual/OrganismPage|Organism Page]] of the selected organism. The '''Feature Table''' will open the [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] and show you the features present in that organism. '''Genome Browser''' leads to the [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] for the selected organism. Clicking '''Scenarios''' shows the [[SEED_Viewer_Manual/Scenarios|Scenarios]] page for your organism. '''Subsystems''' opens a page that lets you select subsystems. '''Export''' enables you to [[SEED_Viewer_Manual/Export|download]] the features of your organism. [[Image:MenuOrganism.png]] === Comparative Tools === This menu is also present whenever an organism is viewed. Different kinds of comparisons of your selected organism to other organisms are available here. '''Function based Comparison''' - The [[SEED_Viewer_Manual/CompareMetabolicReconstruction|Compare Metabolic Reconstruction]] will enable you to see the metabolic reconstruction of your selected organism against that of another one. The '''Sequence based Comparison''' [[SEED_Viewer_Manual/MultiGenomeCompare|Multi Genome Compare]] shows a table and a graphics comparing a selected set of organisms projected against your chosen one (BLAST-based). Use the '''KEGG Metabolic Analysis''' [[SEED_Viewer_Manual/KEGG|to project the metabolic capabilities]] of your organism on KEGG maps. Blasting against your organism is enabled using the '''[[SEED_Viewer_Manual/BLASTOrganism|BLAST Search]]'''. [[Image:CompTools.png]] === Feature Menu === [[Image:MenuFeature]] === Feature Tools == [[Image:MenuFeatTools]] === FIGfams Menu === On SeedViewer pages that deal with [[Glossary#FIGfam|FIGfams]], you will find an additional FIGfams menu. The '''Home''' link leads to the entry page to [[SEED_Viewer_Manual/FIGfams|FIGfams]]. The '''Release History''' will lead you to a [[SEED_Viewer_Manual/FIGfamsRelease|page]] containing a number of statistics about the current release of the FIGfams. '''Download''' will connect you to the FTP server to enable you to download the FIGfams. [[Image:MenuFIGfam.png]] 2a0e8a440b1b8674d0a9498088591eb9d2704cbd 2025 2024 2008-11-24T15:38:33Z DanielaBartels 10 /* Feature Menu */ wikitext text/x-wiki == Menu Overview == === Navigate Menu === This menu is present on every SeedViewer page. The first entry '''Startpage''' will lead to the SeedViewer [[SEED_Viewer_Manual|HomePage]]. '''Organisms''' will open the [[SEED_Viewer_Manual/OrganismSelect|Organism Select]] page. You will see an overview of all organisms in the SEED and are able to select one to view in detail. '''Subsystems''' will do the same for subsystems. '''FIGFams''' leads to an entry point for browsing [[SEED_Viewer_Manual/FIGfams|FIGfams]]. You can find more information about FIGfams [[Glossary#FIGfam|here]]. The '''BLAST Search''' links to the [[SEED_Viewer_Manual/BLASTOrganism|BLAST Page]]. You will be able to BLAST a sequence against an organism in the SEED. [[Image:MenuNav.png]] === Help Menu === This menu is also present on all SeedViewer pages. The first link '''What is the SEED''' will lead you to the [[Home_of_the_SEED|SEED Homepage]]. Clicking the second link '''How to use the SEED Viewer''' will get you to this wiki. '''Submitting data to SEED''' lets you browse the [[RAST_Tutorial|RAST Tutorial]]. '''Contact''' enables you to write an email to the SEED team. Clicking '''Register''' is the first step to get a user account. It will lead to the [[SEED_Viewer_Manual/Register|Register]] page. '''I forgot my password''' enables you to [[SEED_Viewer_Manual/RequestNewPassword|Request a new password]]. [[Image:MenuHelp.png]] === Organism Menu === In the context of a selected organism, an organism menu will appear. '''General Information''' will lead to the [[SEED_Viewer_Manual/OrganismPage|Organism Page]] of the selected organism. The '''Feature Table''' will open the [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] and show you the features present in that organism. '''Genome Browser''' leads to the [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] for the selected organism. Clicking '''Scenarios''' shows the [[SEED_Viewer_Manual/Scenarios|Scenarios]] page for your organism. '''Subsystems''' opens a page that lets you select subsystems. '''Export''' enables you to [[SEED_Viewer_Manual/Export|download]] the features of your organism. [[Image:MenuOrganism.png]] === Comparative Tools === This menu is also present whenever an organism is viewed. Different kinds of comparisons of your selected organism to other organisms are available here. '''Function based Comparison''' - The [[SEED_Viewer_Manual/CompareMetabolicReconstruction|Compare Metabolic Reconstruction]] will enable you to see the metabolic reconstruction of your selected organism against that of another one. The '''Sequence based Comparison''' [[SEED_Viewer_Manual/MultiGenomeCompare|Multi Genome Compare]] shows a table and a graphics comparing a selected set of organisms projected against your chosen one (BLAST-based). Use the '''KEGG Metabolic Analysis''' [[SEED_Viewer_Manual/KEGG|to project the metabolic capabilities]] of your organism on KEGG maps. Blasting against your organism is enabled using the '''[[SEED_Viewer_Manual/BLASTOrganism|BLAST Search]]'''. [[Image:CompTools.png]] === Feature Menu === [[Image:MenuFeature.png]] === Feature Tools == [[Image:MenuFeatTools]] === FIGfams Menu === On SeedViewer pages that deal with [[Glossary#FIGfam|FIGfams]], you will find an additional FIGfams menu. The '''Home''' link leads to the entry page to [[SEED_Viewer_Manual/FIGfams|FIGfams]]. The '''Release History''' will lead you to a [[SEED_Viewer_Manual/FIGfamsRelease|page]] containing a number of statistics about the current release of the FIGfams. '''Download''' will connect you to the FTP server to enable you to download the FIGfams. [[Image:MenuFIGfam.png]] 7d3c0290cfb765b32c89436195bb1183c79feb8f 2026 2025 2008-11-24T15:40:05Z DanielaBartels 10 /* = Feature Tools */ wikitext text/x-wiki == Menu Overview == === Navigate Menu === This menu is present on every SeedViewer page. The first entry '''Startpage''' will lead to the SeedViewer [[SEED_Viewer_Manual|HomePage]]. '''Organisms''' will open the [[SEED_Viewer_Manual/OrganismSelect|Organism Select]] page. You will see an overview of all organisms in the SEED and are able to select one to view in detail. '''Subsystems''' will do the same for subsystems. '''FIGFams''' leads to an entry point for browsing [[SEED_Viewer_Manual/FIGfams|FIGfams]]. You can find more information about FIGfams [[Glossary#FIGfam|here]]. The '''BLAST Search''' links to the [[SEED_Viewer_Manual/BLASTOrganism|BLAST Page]]. You will be able to BLAST a sequence against an organism in the SEED. [[Image:MenuNav.png]] === Help Menu === This menu is also present on all SeedViewer pages. The first link '''What is the SEED''' will lead you to the [[Home_of_the_SEED|SEED Homepage]]. Clicking the second link '''How to use the SEED Viewer''' will get you to this wiki. '''Submitting data to SEED''' lets you browse the [[RAST_Tutorial|RAST Tutorial]]. '''Contact''' enables you to write an email to the SEED team. Clicking '''Register''' is the first step to get a user account. It will lead to the [[SEED_Viewer_Manual/Register|Register]] page. '''I forgot my password''' enables you to [[SEED_Viewer_Manual/RequestNewPassword|Request a new password]]. [[Image:MenuHelp.png]] === Organism Menu === In the context of a selected organism, an organism menu will appear. '''General Information''' will lead to the [[SEED_Viewer_Manual/OrganismPage|Organism Page]] of the selected organism. The '''Feature Table''' will open the [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] and show you the features present in that organism. '''Genome Browser''' leads to the [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] for the selected organism. Clicking '''Scenarios''' shows the [[SEED_Viewer_Manual/Scenarios|Scenarios]] page for your organism. '''Subsystems''' opens a page that lets you select subsystems. '''Export''' enables you to [[SEED_Viewer_Manual/Export|download]] the features of your organism. [[Image:MenuOrganism.png]] === Comparative Tools === This menu is also present whenever an organism is viewed. Different kinds of comparisons of your selected organism to other organisms are available here. '''Function based Comparison''' - The [[SEED_Viewer_Manual/CompareMetabolicReconstruction|Compare Metabolic Reconstruction]] will enable you to see the metabolic reconstruction of your selected organism against that of another one. The '''Sequence based Comparison''' [[SEED_Viewer_Manual/MultiGenomeCompare|Multi Genome Compare]] shows a table and a graphics comparing a selected set of organisms projected against your chosen one (BLAST-based). Use the '''KEGG Metabolic Analysis''' [[SEED_Viewer_Manual/KEGG|to project the metabolic capabilities]] of your organism on KEGG maps. Blasting against your organism is enabled using the '''[[SEED_Viewer_Manual/BLASTOrganism|BLAST Search]]'''. [[Image:CompTools.png]] === Feature Menu === [[Image:MenuFeature.png]] === Feature Tools == [[Image:MenuFeatTools.png]] === FIGfams Menu === On SeedViewer pages that deal with [[Glossary#FIGfam|FIGfams]], you will find an additional FIGfams menu. The '''Home''' link leads to the entry page to [[SEED_Viewer_Manual/FIGfams|FIGfams]]. The '''Release History''' will lead you to a [[SEED_Viewer_Manual/FIGfamsRelease|page]] containing a number of statistics about the current release of the FIGfams. '''Download''' will connect you to the FTP server to enable you to download the FIGfams. [[Image:MenuFIGfam.png]] 2498249e4b08712d87ac5bab11fb641f639f3b5d 6 1504 2027 2008-11-24T15:41:52Z DanielaBartels 10 wikitext text/x-wiki da39a3ee5e6b4b0d3255bfef95601890afd80709 0 1478 2028 2026 2008-11-24T15:46:14Z DanielaBartels 10 /* Feature Menu */ wikitext text/x-wiki == Menu Overview == === Navigate Menu === This menu is present on every SeedViewer page. The first entry '''Startpage''' will lead to the SeedViewer [[SEED_Viewer_Manual|HomePage]]. '''Organisms''' will open the [[SEED_Viewer_Manual/OrganismSelect|Organism Select]] page. You will see an overview of all organisms in the SEED and are able to select one to view in detail. '''Subsystems''' will do the same for subsystems. '''FIGFams''' leads to an entry point for browsing [[SEED_Viewer_Manual/FIGfams|FIGfams]]. You can find more information about FIGfams [[Glossary#FIGfam|here]]. The '''BLAST Search''' links to the [[SEED_Viewer_Manual/BLASTOrganism|BLAST Page]]. You will be able to BLAST a sequence against an organism in the SEED. [[Image:MenuNav.png]] === Help Menu === This menu is also present on all SeedViewer pages. The first link '''What is the SEED''' will lead you to the [[Home_of_the_SEED|SEED Homepage]]. Clicking the second link '''How to use the SEED Viewer''' will get you to this wiki. '''Submitting data to SEED''' lets you browse the [[RAST_Tutorial|RAST Tutorial]]. '''Contact''' enables you to write an email to the SEED team. Clicking '''Register''' is the first step to get a user account. It will lead to the [[SEED_Viewer_Manual/Register|Register]] page. '''I forgot my password''' enables you to [[SEED_Viewer_Manual/RequestNewPassword|Request a new password]]. [[Image:MenuHelp.png]] === Organism Menu === In the context of a selected organism, an organism menu will appear. '''General Information''' will lead to the [[SEED_Viewer_Manual/OrganismPage|Organism Page]] of the selected organism. The '''Feature Table''' will open the [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] and show you the features present in that organism. '''Genome Browser''' leads to the [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] for the selected organism. Clicking '''Scenarios''' shows the [[SEED_Viewer_Manual/Scenarios|Scenarios]] page for your organism. '''Subsystems''' opens a page that lets you select subsystems. '''Export''' enables you to [[SEED_Viewer_Manual/Export|download]] the features of your organism. [[Image:MenuOrganism.png]] === Comparative Tools === This menu is also present whenever an organism is viewed. Different kinds of comparisons of your selected organism to other organisms are available here. '''Function based Comparison''' - The [[SEED_Viewer_Manual/CompareMetabolicReconstruction|Compare Metabolic Reconstruction]] will enable you to see the metabolic reconstruction of your selected organism against that of another one. The '''Sequence based Comparison''' [[SEED_Viewer_Manual/MultiGenomeCompare|Multi Genome Compare]] shows a table and a graphics comparing a selected set of organisms projected against your chosen one (BLAST-based). Use the '''KEGG Metabolic Analysis''' [[SEED_Viewer_Manual/KEGG|to project the metabolic capabilities]] of your organism on KEGG maps. Blasting against your organism is enabled using the '''[[SEED_Viewer_Manual/BLASTOrganism|BLAST Search]]'''. [[Image:CompTools.png]] === Feature Menu === Whenever a feature is defined on a SeedViewer page, you will find the '''Feature''' menu for that feature. The '''Feature Overview''' points to the [[SEED_Viewer_Manual/Annotation|Annotation]] page. It shows general information about the feature, als well as a Compare Regions View that displays the feature in its genomic context and in comparison to homologs in other genomes. [[Image:MenuFeature.png]] === Feature Tools == [[Image:MenuFeatTools.png]] === FIGfams Menu === On SeedViewer pages that deal with [[Glossary#FIGfam|FIGfams]], you will find an additional FIGfams menu. The '''Home''' link leads to the entry page to [[SEED_Viewer_Manual/FIGfams|FIGfams]]. The '''Release History''' will lead you to a [[SEED_Viewer_Manual/FIGfamsRelease|page]] containing a number of statistics about the current release of the FIGfams. '''Download''' will connect you to the FTP server to enable you to download the FIGfams. [[Image:MenuFIGfam.png]] 7c1dfe8a301290af4e256bf9be19df1f78bf7151 2029 2028 2008-11-24T15:54:36Z DanielaBartels 10 /* Feature Menu */ wikitext text/x-wiki == Menu Overview == === Navigate Menu === This menu is present on every SeedViewer page. The first entry '''Startpage''' will lead to the SeedViewer [[SEED_Viewer_Manual|HomePage]]. '''Organisms''' will open the [[SEED_Viewer_Manual/OrganismSelect|Organism Select]] page. You will see an overview of all organisms in the SEED and are able to select one to view in detail. '''Subsystems''' will do the same for subsystems. '''FIGFams''' leads to an entry point for browsing [[SEED_Viewer_Manual/FIGfams|FIGfams]]. You can find more information about FIGfams [[Glossary#FIGfam|here]]. The '''BLAST Search''' links to the [[SEED_Viewer_Manual/BLASTOrganism|BLAST Page]]. You will be able to BLAST a sequence against an organism in the SEED. [[Image:MenuNav.png]] === Help Menu === This menu is also present on all SeedViewer pages. The first link '''What is the SEED''' will lead you to the [[Home_of_the_SEED|SEED Homepage]]. Clicking the second link '''How to use the SEED Viewer''' will get you to this wiki. '''Submitting data to SEED''' lets you browse the [[RAST_Tutorial|RAST Tutorial]]. '''Contact''' enables you to write an email to the SEED team. Clicking '''Register''' is the first step to get a user account. It will lead to the [[SEED_Viewer_Manual/Register|Register]] page. '''I forgot my password''' enables you to [[SEED_Viewer_Manual/RequestNewPassword|Request a new password]]. [[Image:MenuHelp.png]] === Organism Menu === In the context of a selected organism, an organism menu will appear. '''General Information''' will lead to the [[SEED_Viewer_Manual/OrganismPage|Organism Page]] of the selected organism. The '''Feature Table''' will open the [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] and show you the features present in that organism. '''Genome Browser''' leads to the [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] for the selected organism. Clicking '''Scenarios''' shows the [[SEED_Viewer_Manual/Scenarios|Scenarios]] page for your organism. '''Subsystems''' opens a page that lets you select subsystems. '''Export''' enables you to [[SEED_Viewer_Manual/Export|download]] the features of your organism. [[Image:MenuOrganism.png]] === Comparative Tools === This menu is also present whenever an organism is viewed. Different kinds of comparisons of your selected organism to other organisms are available here. '''Function based Comparison''' - The [[SEED_Viewer_Manual/CompareMetabolicReconstruction|Compare Metabolic Reconstruction]] will enable you to see the metabolic reconstruction of your selected organism against that of another one. The '''Sequence based Comparison''' [[SEED_Viewer_Manual/MultiGenomeCompare|Multi Genome Compare]] shows a table and a graphics comparing a selected set of organisms projected against your chosen one (BLAST-based). Use the '''KEGG Metabolic Analysis''' [[SEED_Viewer_Manual/KEGG|to project the metabolic capabilities]] of your organism on KEGG maps. Blasting against your organism is enabled using the '''[[SEED_Viewer_Manual/BLASTOrganism|BLAST Search]]'''. [[Image:CompTools.png]] === Feature Menu === Whenever a feature is defined on a SeedViewer page, you will find the '''Feature''' menu for that feature. The '''Feature Overview''' points to the [[SEED_Viewer_Manual/Annotation|Annotation]] page. It shows general information about the feature, als well as a Compare Regions View that displays the feature in its genomic context and in comparison to homologs in other genomes. '''DNA Sequence''' will open a page with the DNA Sequence of the feature (in FASTA format). '''DNA w/ flanking''' not only prints the DNA sequence of the feature, but also includes a user-defined number of bases upstream and downstream of the feature. '''Protein Sequence''' will show you the protein FASTA sequence (translated from the DNA sequence) of the feature. '''Feature Evidence vs. FIG''' and '''Feature Evidence vs. all DB''' link to the [[SEED_Viewer_Manual/Evidence|Evidence]] page. The difference between the two is that the evidence shown for the feature includes only evidence against features in the SEED or also against other databases (e.g. GenBank, SwissProt, UniProt and many others). The evidence page will also allow you to make this selection or change it there. [[Image:MenuFeature.png]] === Feature Tools == [[Image:MenuFeatTools.png]] === FIGfams Menu === On SeedViewer pages that deal with [[Glossary#FIGfam|FIGfams]], you will find an additional FIGfams menu. The '''Home''' link leads to the entry page to [[SEED_Viewer_Manual/FIGfams|FIGfams]]. The '''Release History''' will lead you to a [[SEED_Viewer_Manual/FIGfamsRelease|page]] containing a number of statistics about the current release of the FIGfams. '''Download''' will connect you to the FTP server to enable you to download the FIGfams. [[Image:MenuFIGfam.png]] 4d119372b54da1acd6c2fb25f9f9225e612e1a22 2031 2029 2008-11-24T15:59:23Z DanielaBartels 10 /* = Feature Tools */ wikitext text/x-wiki == Menu Overview == === Navigate Menu === This menu is present on every SeedViewer page. The first entry '''Startpage''' will lead to the SeedViewer [[SEED_Viewer_Manual|HomePage]]. '''Organisms''' will open the [[SEED_Viewer_Manual/OrganismSelect|Organism Select]] page. You will see an overview of all organisms in the SEED and are able to select one to view in detail. '''Subsystems''' will do the same for subsystems. '''FIGFams''' leads to an entry point for browsing [[SEED_Viewer_Manual/FIGfams|FIGfams]]. You can find more information about FIGfams [[Glossary#FIGfam|here]]. The '''BLAST Search''' links to the [[SEED_Viewer_Manual/BLASTOrganism|BLAST Page]]. You will be able to BLAST a sequence against an organism in the SEED. [[Image:MenuNav.png]] === Help Menu === This menu is also present on all SeedViewer pages. The first link '''What is the SEED''' will lead you to the [[Home_of_the_SEED|SEED Homepage]]. Clicking the second link '''How to use the SEED Viewer''' will get you to this wiki. '''Submitting data to SEED''' lets you browse the [[RAST_Tutorial|RAST Tutorial]]. '''Contact''' enables you to write an email to the SEED team. Clicking '''Register''' is the first step to get a user account. It will lead to the [[SEED_Viewer_Manual/Register|Register]] page. '''I forgot my password''' enables you to [[SEED_Viewer_Manual/RequestNewPassword|Request a new password]]. [[Image:MenuHelp.png]] === Organism Menu === In the context of a selected organism, an organism menu will appear. '''General Information''' will lead to the [[SEED_Viewer_Manual/OrganismPage|Organism Page]] of the selected organism. The '''Feature Table''' will open the [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] and show you the features present in that organism. '''Genome Browser''' leads to the [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] for the selected organism. Clicking '''Scenarios''' shows the [[SEED_Viewer_Manual/Scenarios|Scenarios]] page for your organism. '''Subsystems''' opens a page that lets you select subsystems. '''Export''' enables you to [[SEED_Viewer_Manual/Export|download]] the features of your organism. [[Image:MenuOrganism.png]] === Comparative Tools === This menu is also present whenever an organism is viewed. Different kinds of comparisons of your selected organism to other organisms are available here. '''Function based Comparison''' - The [[SEED_Viewer_Manual/CompareMetabolicReconstruction|Compare Metabolic Reconstruction]] will enable you to see the metabolic reconstruction of your selected organism against that of another one. The '''Sequence based Comparison''' [[SEED_Viewer_Manual/MultiGenomeCompare|Multi Genome Compare]] shows a table and a graphics comparing a selected set of organisms projected against your chosen one (BLAST-based). Use the '''KEGG Metabolic Analysis''' [[SEED_Viewer_Manual/KEGG|to project the metabolic capabilities]] of your organism on KEGG maps. Blasting against your organism is enabled using the '''[[SEED_Viewer_Manual/BLASTOrganism|BLAST Search]]'''. [[Image:CompTools.png]] === Feature Menu === Whenever a feature is defined on a SeedViewer page, you will find the '''Feature''' menu for that feature. The '''Feature Overview''' points to the [[SEED_Viewer_Manual/Annotation|Annotation]] page. It shows general information about the feature, als well as a Compare Regions View that displays the feature in its genomic context and in comparison to homologs in other genomes. '''DNA Sequence''' will open a page with the DNA Sequence of the feature (in FASTA format). '''DNA w/ flanking''' not only prints the DNA sequence of the feature, but also includes a user-defined number of bases upstream and downstream of the feature. '''Protein Sequence''' will show you the protein FASTA sequence (translated from the DNA sequence) of the feature. '''Feature Evidence vs. FIG''' and '''Feature Evidence vs. all DB''' link to the [[SEED_Viewer_Manual/Evidence|Evidence]] page. The difference between the two is that the evidence shown for the feature includes only evidence against features in the SEED or also against other databases (e.g. GenBank, SwissProt, UniProt and many others). The evidence page will also allow you to make this selection or change it there. [[Image:MenuFeature.png]] === Feature Tools === This menu is also present if a feature is defined. It lets the user run a variaty of tools using the feature sequence. These include tools that look for transmembrane helices (e.t. TMHMM), signal peptides (PSORT, SignalP), protein domains (e.g. InterPro, ProDom) and others. [[Image:MenuFeatTools.png]] === FIGfams Menu === On SeedViewer pages that deal with [[Glossary#FIGfam|FIGfams]], you will find an additional FIGfams menu. The '''Home''' link leads to the entry page to [[SEED_Viewer_Manual/FIGfams|FIGfams]]. The '''Release History''' will lead you to a [[SEED_Viewer_Manual/FIGfamsRelease|page]] containing a number of statistics about the current release of the FIGfams. '''Download''' will connect you to the FTP server to enable you to download the FIGfams. [[Image:MenuFIGfam.png]] fd8ff03ec969c009fbcbf9fd5619e074b2dc87c0 0 1466 2030 2021 2008-11-24T15:55:49Z DanielaBartels 10 /* Evidence */ wikitext text/x-wiki == Main pages of the SeedViewer == ''' [[SEED_Viewer_Manual|Home Page]] ''' ''' [[SEED_Viewer_Manual|Menu]] ''' === Subsystem Select === === Subsystems === === Functional Role === === FigFams === '''[[SEED_Viewer_Manual/Annotation|Annotation]]''' '''[[SEED_Viewer_Manual/Evidence|Evidence]]''' '''[[SEED_Viewer_Manual/BLASTOrganism|BLAST against an organism]]''' === Sequence === '''[[SEED_Viewer_Manual/GenomeBrowser|Browse Genome]]''' '''[[SEED_Viewer_Manual/OrganismSelect|Organism Select]]''' '''[[SEED_Viewer_Manual/OrganismPage|Organism Page]]''' === Kegg === '''[[SEED_Viewer_Manual/HomologClusters|Homolog Clusters]]''' 232d7d3f6861332e1575540095c513eb33694a61 2037 2030 2008-11-24T16:10:27Z DanielaBartels 10 /* Main pages of the SeedViewer */ wikitext text/x-wiki == Main pages of the SeedViewer == ''' [[SEED_Viewer_Manual|Home Page]] ''' ''' [[SEED_Viewer_Manual/Menu|Menu]] ''' === Subsystem Select === === Subsystems === === Functional Role === === FigFams === '''[[SEED_Viewer_Manual/Annotation|Annotation]]''' '''[[SEED_Viewer_Manual/Evidence|Evidence]]''' '''[[SEED_Viewer_Manual/BLASTOrganism|BLAST against an organism]]''' === Sequence === '''[[SEED_Viewer_Manual/GenomeBrowser|Browse Genome]]''' '''[[SEED_Viewer_Manual/OrganismSelect|Organism Select]]''' '''[[SEED_Viewer_Manual/OrganismPage|Organism Page]]''' === Kegg === '''[[SEED_Viewer_Manual/HomologClusters|Homolog Clusters]]''' 0e2916bf51894b25c77343c38107870fc6352dc2 0 1502 2032 2022 2008-11-24T16:03:45Z DanielaBartels 10 /* Domains */ wikitext text/x-wiki The Evidence Page is divided into two parts via a [[WebComponents/Tabview|TabView]]: The '''Visual Protein Evidence''' and the '''Tabular Protein Evidence'''. == Visual Protein Evidence == === Location === === Domains === [[Image:EvidenceDomains.png]] === Similarities === == Tabular Protein Evidence == === Similarities === === Domains === === Identical Proteins === === Functionally Coupled === f3c917f7c8c02251f10dd55bd519d7c4d75b3887 2034 2032 2008-11-24T16:04:43Z DanielaBartels 10 /* Domains */ wikitext text/x-wiki The Evidence Page is divided into two parts via a [[WebComponents/Tabview|TabView]]: The '''Visual Protein Evidence''' and the '''Tabular Protein Evidence'''. == Visual Protein Evidence == === Location === === Domains === [[Image:EvidenceDomain.png]] === Similarities === == Tabular Protein Evidence == === Similarities === === Domains === === Identical Proteins === === Functionally Coupled === 3ad62b60bf8212922ba52932d0d6d3998311dd3a 2036 2034 2008-11-24T16:07:45Z DanielaBartels 10 /* Domains */ wikitext text/x-wiki The Evidence Page is divided into two parts via a [[WebComponents/Tabview|TabView]]: The '''Visual Protein Evidence''' and the '''Tabular Protein Evidence'''. == Visual Protein Evidence == === Location === === Domains === This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the whole length of the protein). [[Image:EvidenceDomain.png]] === Similarities === == Tabular Protein Evidence == === Similarities === === Domains === === Identical Proteins === === Functionally Coupled === 2eedf81d29caa4c4aeca2b725b90889fe9ec6ef5 2038 2036 2008-11-24T16:10:51Z DanielaBartels 10 /* Domains */ wikitext text/x-wiki The Evidence Page is divided into two parts via a [[WebComponents/Tabview|TabView]]: The '''Visual Protein Evidence''' and the '''Tabular Protein Evidence'''. == Visual Protein Evidence == === Location === === Domains === This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the whole length of the protein). Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]] in the menu bar. [[Image:EvidenceDomain.png]] === Similarities === == Tabular Protein Evidence == === Similarities === === Domains === === Identical Proteins === === Functionally Coupled === 439a764b1f7489ed81f43e93ebe56b319a9534d9 2039 2038 2008-11-24T16:17:02Z DanielaBartels 10 wikitext text/x-wiki The Evidence Page is divided into two parts via a [[WebComponents/Tabview|TabView]]: The '''Visual Protein Evidence''' and the '''Tabular Protein Evidence'''. == Visual Protein Evidence == === Location === === Domains === This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the whole length of the protein). Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]] in the menu bar. [[Image:EvidenceDomain.png]] === Similarities === == Tabular Protein Evidence == === Similarities === === Domains === This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the whole length of the protein). The table lists the '''Domain DB'' (the database for the domain that was hit), the '''ID''' in the domain database, the '''Name''' of the domain, the '''Location''' of the hit in the selected feature, the '''Score''' for the hit against the domain, as well as the '''Function''' of the domain. Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]] in the menu bar. [[Image:EvidenceDomain.png]] === Identical Proteins === === Functionally Coupled === c57e9a59f7eccabc67e4f11206a703ca8fac69a2 2040 2039 2008-11-24T16:17:19Z DanielaBartels 10 /* Domains */ wikitext text/x-wiki The Evidence Page is divided into two parts via a [[WebComponents/Tabview|TabView]]: The '''Visual Protein Evidence''' and the '''Tabular Protein Evidence'''. == Visual Protein Evidence == === Location === === Domains === This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the whole length of the protein). Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]] in the menu bar. [[Image:EvidenceDomain.png]] === Similarities === == Tabular Protein Evidence == === Similarities === === Domains === This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the whole length of the protein). The table lists the '''Domain DB'' (the database for the domain that was hit), the '''ID''' in the domain database, the '''Name''' of the domain, the '''Location''' of the hit in the selected feature, the '''Score''' for the hit against the domain, as well as the '''Function''' of the domain. Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]] in the menu bar. [[Image:EvidenceDomTable.png]] === Identical Proteins === === Functionally Coupled === b057eac6179705f7e732c367f18a96298edaffed 2042 2040 2008-11-24T16:18:50Z DanielaBartels 10 /* Domains */ wikitext text/x-wiki The Evidence Page is divided into two parts via a [[WebComponents/Tabview|TabView]]: The '''Visual Protein Evidence''' and the '''Tabular Protein Evidence'''. == Visual Protein Evidence == === Location === === Domains === This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the whole length of the protein). Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]] in the menu bar. [[Image:EvidenceDomain.png]] === Similarities === == Tabular Protein Evidence == === Similarities === === Domains === This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the whole length of the protein). The table lists the '''Domain DB''' (the database for the domain that was hit), the '''ID''' in the domain database, the '''Name''' of the domain, the '''Location''' of the hit in the selected feature, the '''Score''' for the hit against the domain, as well as the '''Function''' of the domain. The table can be exported using the '''export table''' button. Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]] in the menu bar. [[Image:EvidenceDomTable.png]] === Identical Proteins === === Functionally Coupled === 359bccf9aa7c6b05b784a25e24baa29c84741f0c 2043 2042 2008-11-24T16:19:24Z DanielaBartels 10 /* Domains */ wikitext text/x-wiki The Evidence Page is divided into two parts via a [[WebComponents/Tabview|TabView]]: The '''Visual Protein Evidence''' and the '''Tabular Protein Evidence'''. == Visual Protein Evidence == === Location === === Domains === This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the whole length of the protein). Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]] in the menu bar. [[Image:EvidenceDomain.png]] === Similarities === == Tabular Protein Evidence == === Similarities === === Domains === This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the whole length of the protein). The [[WebComponents/Table|table]] lists the '''Domain DB''' (the database for the domain that was hit), the '''ID''' in the domain database, the '''Name''' of the domain, the '''Location''' of the hit in the selected feature, the '''Score''' for the hit against the domain, as well as the '''Function''' of the domain. The table can be exported using the '''export table''' button. Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]] in the menu bar. [[Image:EvidenceDomTable.png]] === Identical Proteins === === Functionally Coupled === c3585c43c54a577ce2a822376fceae9dbc9080b3 2044 2043 2008-11-24T16:22:37Z DanielaBartels 10 /* Location */ wikitext text/x-wiki The Evidence Page is divided into two parts via a [[WebComponents/Tabview|TabView]]: The '''Visual Protein Evidence''' and the '''Tabular Protein Evidence'''. == Visual Protein Evidence == === Location === [[Image:EvidenceLocation.png]] === Domains === This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the whole length of the protein). Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]] in the menu bar. [[Image:EvidenceDomain.png]] === Similarities === == Tabular Protein Evidence == === Similarities === === Domains === This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the whole length of the protein). The [[WebComponents/Table|table]] lists the '''Domain DB''' (the database for the domain that was hit), the '''ID''' in the domain database, the '''Name''' of the domain, the '''Location''' of the hit in the selected feature, the '''Score''' for the hit against the domain, as well as the '''Function''' of the domain. The table can be exported using the '''export table''' button. Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]] in the menu bar. [[Image:EvidenceDomTable.png]] === Identical Proteins === === Functionally Coupled === 7964e38d395ee95776821d9c8f68aa4e54732fec 2046 2044 2008-11-24T16:29:31Z DanielaBartels 10 wikitext text/x-wiki The Evidence Page is divided into two parts via a [[WebComponents/Tabview|TabView]]: The '''Visual Protein Evidence''' and the '''Tabular Protein Evidence'''. == Visual Protein Evidence == === Location === '''Location''' stand for location of the product of the feature in the cell. This section presents output for tools that look for transmembrane helices or signal peptides in the feature. In the example, you can see five transmembrane helices in the protein identified by the Phobius tool. They are visualized as little boxes, and their location on the line depicts the location of the transmembrane helices in the protein. [[Image:EvidenceLocation.png]] === Domains === This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the whole length of the protein). Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]] in the menu bar. [[Image:EvidenceDomain.png]] === Similarities === == Tabular Protein Evidence == === Similarities === === Domains === This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the whole length of the protein). The [[WebComponents/Table|table]] lists the '''Domain DB''' (the database for the domain that was hit), the '''ID''' in the domain database, the '''Name''' of the domain, the '''Location''' of the hit in the selected feature, the '''Score''' for the hit against the domain, as well as the '''Function''' of the domain. The table can be exported using the '''export table''' button. Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]] in the menu bar. [[Image:EvidenceDomTable.png]] === Identical Proteins === === Functionally Coupled === 708f3b92aee0c2876dc7d599afe0faa695d78df1 2047 2046 2008-11-24T16:30:34Z DanielaBartels 10 /* Location */ wikitext text/x-wiki The Evidence Page is divided into two parts via a [[WebComponents/Tabview|TabView]]: The '''Visual Protein Evidence''' and the '''Tabular Protein Evidence'''. == Visual Protein Evidence == === Location === '''Location''' stand for location of the product of the feature in the cell. This section presents output for tools that look for transmembrane helices (TM) or signal peptides (SP) in the feature. In the example, you can see five transmembrane helices in the protein identified by the Phobius tool. They are visualized as little boxes, and their location on the line depicts the location of the transmembrane helices in the protein. [[Image:EvidenceLocation.png]] === Domains === This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the whole length of the protein). Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]] in the menu bar. [[Image:EvidenceDomain.png]] === Similarities === == Tabular Protein Evidence == === Similarities === === Domains === This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the whole length of the protein). The [[WebComponents/Table|table]] lists the '''Domain DB''' (the database for the domain that was hit), the '''ID''' in the domain database, the '''Name''' of the domain, the '''Location''' of the hit in the selected feature, the '''Score''' for the hit against the domain, as well as the '''Function''' of the domain. The table can be exported using the '''export table''' button. Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]] in the menu bar. [[Image:EvidenceDomTable.png]] === Identical Proteins === === Functionally Coupled === 28985cb1637d6e06a7aafcf8ba963a8ae44885a5 2048 2047 2008-11-24T16:33:01Z DanielaBartels 10 /* Identical Proteins */ wikitext text/x-wiki The Evidence Page is divided into two parts via a [[WebComponents/Tabview|TabView]]: The '''Visual Protein Evidence''' and the '''Tabular Protein Evidence'''. == Visual Protein Evidence == === Location === '''Location''' stand for location of the product of the feature in the cell. This section presents output for tools that look for transmembrane helices (TM) or signal peptides (SP) in the feature. In the example, you can see five transmembrane helices in the protein identified by the Phobius tool. They are visualized as little boxes, and their location on the line depicts the location of the transmembrane helices in the protein. [[Image:EvidenceLocation.png]] === Domains === This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the whole length of the protein). Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]] in the menu bar. [[Image:EvidenceDomain.png]] === Similarities === == Tabular Protein Evidence == === Similarities === === Domains === This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the whole length of the protein). The [[WebComponents/Table|table]] lists the '''Domain DB''' (the database for the domain that was hit), the '''ID''' in the domain database, the '''Name''' of the domain, the '''Location''' of the hit in the selected feature, the '''Score''' for the hit against the domain, as well as the '''Function''' of the domain. The table can be exported using the '''export table''' button. Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]] in the menu bar. [[Image:EvidenceDomTable.png]] === Identical Proteins === [[Image:EvidenceEIPs.png]] === Functionally Coupled === f6008c809dd217cba73ab6917a45dfec234fd3e9 2050 2048 2008-11-24T16:42:39Z DanielaBartels 10 /* Identical Proteins */ wikitext text/x-wiki The Evidence Page is divided into two parts via a [[WebComponents/Tabview|TabView]]: The '''Visual Protein Evidence''' and the '''Tabular Protein Evidence'''. == Visual Protein Evidence == === Location === '''Location''' stand for location of the product of the feature in the cell. This section presents output for tools that look for transmembrane helices (TM) or signal peptides (SP) in the feature. In the example, you can see five transmembrane helices in the protein identified by the Phobius tool. They are visualized as little boxes, and their location on the line depicts the location of the transmembrane helices in the protein. [[Image:EvidenceLocation.png]] === Domains === This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the whole length of the protein). Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]] in the menu bar. [[Image:EvidenceDomain.png]] === Similarities === == Tabular Protein Evidence == === Similarities === === Domains === This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the whole length of the protein). The [[WebComponents/Table|table]] lists the '''Domain DB''' (the database for the domain that was hit), the '''ID''' in the domain database, the '''Name''' of the domain, the '''Location''' of the hit in the selected feature, the '''Score''' for the hit against the domain, as well as the '''Function''' of the domain. The table can be exported using the '''export table''' button. Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]] in the menu bar. [[Image:EvidenceDomTable.png]] === Identical Proteins === '''Essentially Identical Proteins''' are proteins that share a common sequence, but the start position of the proteins may vary a little. This definition was made because in different databases or close strains of organisms, it often happens that a protein is present, but the start position may be shifted in the finding genes step. So essentially, this table shows aliases of the feature that were based on protein identity. The first column of the [[WebComponents/Table|table]] shows the '''Database''' the alias can be found in, while the second column ('''ID''') offers the alias name and a link to the protein in the respective database. The following two columns describe the '''Organism''' and the '''Assignment''' for the feature for the alias. [[Image:EvidenceEIPs.png]] === Functionally Coupled === 8dfecc904fe2dd027858d60f02e7f0af3c62357e 2051 2050 2008-11-24T16:44:40Z DanielaBartels 10 /* Functionally Coupled */ wikitext text/x-wiki The Evidence Page is divided into two parts via a [[WebComponents/Tabview|TabView]]: The '''Visual Protein Evidence''' and the '''Tabular Protein Evidence'''. == Visual Protein Evidence == === Location === '''Location''' stand for location of the product of the feature in the cell. This section presents output for tools that look for transmembrane helices (TM) or signal peptides (SP) in the feature. In the example, you can see five transmembrane helices in the protein identified by the Phobius tool. They are visualized as little boxes, and their location on the line depicts the location of the transmembrane helices in the protein. [[Image:EvidenceLocation.png]] === Domains === This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the whole length of the protein). Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]] in the menu bar. [[Image:EvidenceDomain.png]] === Similarities === == Tabular Protein Evidence == === Similarities === === Domains === This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the whole length of the protein). The [[WebComponents/Table|table]] lists the '''Domain DB''' (the database for the domain that was hit), the '''ID''' in the domain database, the '''Name''' of the domain, the '''Location''' of the hit in the selected feature, the '''Score''' for the hit against the domain, as well as the '''Function''' of the domain. The table can be exported using the '''export table''' button. Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]] in the menu bar. [[Image:EvidenceDomTable.png]] === Identical Proteins === '''Essentially Identical Proteins''' are proteins that share a common sequence, but the start position of the proteins may vary a little. This definition was made because in different databases or close strains of organisms, it often happens that a protein is present, but the start position may be shifted in the finding genes step. So essentially, this table shows aliases of the feature that were based on protein identity. The first column of the [[WebComponents/Table|table]] shows the '''Database''' the alias can be found in, while the second column ('''ID''') offers the alias name and a link to the protein in the respective database. The following two columns describe the '''Organism''' and the '''Assignment''' for the feature for the alias. [[Image:EvidenceEIPs.png]] === Functionally Coupled === [[Image:EvidenceFC.png]] 798f03235f27a4cfd80aa7cf2688953ed8ccb858 2053 2051 2008-11-24T16:46:08Z DanielaBartels 10 /* Functionally Coupled */ wikitext text/x-wiki The Evidence Page is divided into two parts via a [[WebComponents/Tabview|TabView]]: The '''Visual Protein Evidence''' and the '''Tabular Protein Evidence'''. == Visual Protein Evidence == === Location === '''Location''' stand for location of the product of the feature in the cell. This section presents output for tools that look for transmembrane helices (TM) or signal peptides (SP) in the feature. In the example, you can see five transmembrane helices in the protein identified by the Phobius tool. They are visualized as little boxes, and their location on the line depicts the location of the transmembrane helices in the protein. [[Image:EvidenceLocation.png]] === Domains === This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the whole length of the protein). Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]] in the menu bar. [[Image:EvidenceDomain.png]] === Similarities === == Tabular Protein Evidence == === Similarities === === Domains === This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the whole length of the protein). The [[WebComponents/Table|table]] lists the '''Domain DB''' (the database for the domain that was hit), the '''ID''' in the domain database, the '''Name''' of the domain, the '''Location''' of the hit in the selected feature, the '''Score''' for the hit against the domain, as well as the '''Function''' of the domain. The table can be exported using the '''export table''' button. Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]] in the menu bar. [[Image:EvidenceDomTable.png]] === Identical Proteins === '''Essentially Identical Proteins''' are proteins that share a common sequence, but the start position of the proteins may vary a little. This definition was made because in different databases or close strains of organisms, it often happens that a protein is present, but the start position may be shifted in the finding genes step. So essentially, this table shows aliases of the feature that were based on protein identity. The first column of the [[WebComponents/Table|table]] shows the '''Database''' the alias can be found in, while the second column ('''ID''') offers the alias name and a link to the protein in the respective database. The following two columns describe the '''Organism''' and the '''Assignment''' for the feature for the alias. [[Image:EvidenceEIPs.png]] === Functionally Coupled === [[Image:EvidenceFCs.png]] ee7ed31c0a9fc025d7e33351572d318233903a00 2055 2053 2008-11-24T16:58:20Z DanielaBartels 10 /* Functionally Coupled */ wikitext text/x-wiki The Evidence Page is divided into two parts via a [[WebComponents/Tabview|TabView]]: The '''Visual Protein Evidence''' and the '''Tabular Protein Evidence'''. == Visual Protein Evidence == === Location === '''Location''' stand for location of the product of the feature in the cell. This section presents output for tools that look for transmembrane helices (TM) or signal peptides (SP) in the feature. In the example, you can see five transmembrane helices in the protein identified by the Phobius tool. They are visualized as little boxes, and their location on the line depicts the location of the transmembrane helices in the protein. [[Image:EvidenceLocation.png]] === Domains === This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the whole length of the protein). Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]] in the menu bar. [[Image:EvidenceDomain.png]] === Similarities === == Tabular Protein Evidence == === Similarities === === Domains === This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the whole length of the protein). The [[WebComponents/Table|table]] lists the '''Domain DB''' (the database for the domain that was hit), the '''ID''' in the domain database, the '''Name''' of the domain, the '''Location''' of the hit in the selected feature, the '''Score''' for the hit against the domain, as well as the '''Function''' of the domain. The table can be exported using the '''export table''' button. Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]] in the menu bar. [[Image:EvidenceDomTable.png]] === Identical Proteins === '''Essentially Identical Proteins''' are proteins that share a common sequence, but the start position of the proteins may vary a little. This definition was made because in different databases or close strains of organisms, it often happens that a protein is present, but the start position may be shifted in the finding genes step. So essentially, this table shows aliases of the feature that were based on protein identity. The first column of the [[WebComponents/Table|table]] shows the '''Database''' the alias can be found in, while the second column ('''ID''') offers the alias name and a link to the protein in the respective database. The following two columns describe the '''Organism''' and the '''Assignment''' for the feature for the alias. [[Image:EvidenceEIPs.png]] === Functionally Coupled === This [[WebComponent/Table|table]] lists all [[Glossary/Functional coupling|functionally coupled] genes in the organism. You can see the '''Score''', the '''ID''' of the feature and the '''Function''' of the feature. [[Image:EvidenceFCs.png]] 198191b8b3cef35342281c4247530c20bfe670cd 2056 2055 2008-11-24T16:58:36Z DanielaBartels 10 /* Functionally Coupled */ wikitext text/x-wiki The Evidence Page is divided into two parts via a [[WebComponents/Tabview|TabView]]: The '''Visual Protein Evidence''' and the '''Tabular Protein Evidence'''. == Visual Protein Evidence == === Location === '''Location''' stand for location of the product of the feature in the cell. This section presents output for tools that look for transmembrane helices (TM) or signal peptides (SP) in the feature. In the example, you can see five transmembrane helices in the protein identified by the Phobius tool. They are visualized as little boxes, and their location on the line depicts the location of the transmembrane helices in the protein. [[Image:EvidenceLocation.png]] === Domains === This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the whole length of the protein). Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]] in the menu bar. [[Image:EvidenceDomain.png]] === Similarities === == Tabular Protein Evidence == === Similarities === === Domains === This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the whole length of the protein). The [[WebComponents/Table|table]] lists the '''Domain DB''' (the database for the domain that was hit), the '''ID''' in the domain database, the '''Name''' of the domain, the '''Location''' of the hit in the selected feature, the '''Score''' for the hit against the domain, as well as the '''Function''' of the domain. The table can be exported using the '''export table''' button. Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]] in the menu bar. [[Image:EvidenceDomTable.png]] === Identical Proteins === '''Essentially Identical Proteins''' are proteins that share a common sequence, but the start position of the proteins may vary a little. This definition was made because in different databases or close strains of organisms, it often happens that a protein is present, but the start position may be shifted in the finding genes step. So essentially, this table shows aliases of the feature that were based on protein identity. The first column of the [[WebComponents/Table|table]] shows the '''Database''' the alias can be found in, while the second column ('''ID''') offers the alias name and a link to the protein in the respective database. The following two columns describe the '''Organism''' and the '''Assignment''' for the feature for the alias. [[Image:EvidenceEIPs.png]] === Functionally Coupled === This [[WebComponent/Table|table]] lists all [[Glossary/Functional coupling|functionally coupled]] genes in the organism. You can see the '''Score''', the '''ID''' of the feature and the '''Function''' of the feature. [[Image:EvidenceFCs.png]] 373107ad07dfe10030b8779d7c3f185bda0bbe57 2057 2056 2008-11-24T16:59:16Z DanielaBartels 10 /* Functionally Coupled */ wikitext text/x-wiki The Evidence Page is divided into two parts via a [[WebComponents/Tabview|TabView]]: The '''Visual Protein Evidence''' and the '''Tabular Protein Evidence'''. == Visual Protein Evidence == === Location === '''Location''' stand for location of the product of the feature in the cell. This section presents output for tools that look for transmembrane helices (TM) or signal peptides (SP) in the feature. In the example, you can see five transmembrane helices in the protein identified by the Phobius tool. They are visualized as little boxes, and their location on the line depicts the location of the transmembrane helices in the protein. [[Image:EvidenceLocation.png]] === Domains === This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the whole length of the protein). Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]] in the menu bar. [[Image:EvidenceDomain.png]] === Similarities === == Tabular Protein Evidence == === Similarities === === Domains === This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the whole length of the protein). The [[WebComponents/Table|table]] lists the '''Domain DB''' (the database for the domain that was hit), the '''ID''' in the domain database, the '''Name''' of the domain, the '''Location''' of the hit in the selected feature, the '''Score''' for the hit against the domain, as well as the '''Function''' of the domain. The table can be exported using the '''export table''' button. Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]] in the menu bar. [[Image:EvidenceDomTable.png]] === Identical Proteins === '''Essentially Identical Proteins''' are proteins that share a common sequence, but the start position of the proteins may vary a little. This definition was made because in different databases or close strains of organisms, it often happens that a protein is present, but the start position may be shifted in the finding genes step. So essentially, this table shows aliases of the feature that were based on protein identity. The first column of the [[WebComponents/Table|table]] shows the '''Database''' the alias can be found in, while the second column ('''ID''') offers the alias name and a link to the protein in the respective database. The following two columns describe the '''Organism''' and the '''Assignment''' for the feature for the alias. [[Image:EvidenceEIPs.png]] === Functionally Coupled === This [[WebComponent/Table|table]] lists all [[Glossary#Functional coupling|functionally coupled]] genes in the organism. You can see the '''Score''', the '''ID''' of the feature and the '''Function''' of the feature. [[Image:EvidenceFCs.png]] a08306dc2f194e9c55f378e01e868f3141477c84 2058 2057 2008-11-25T10:04:05Z DanielaBartels 10 /* Similarities */ wikitext text/x-wiki The Evidence Page is divided into two parts via a [[WebComponents/Tabview|TabView]]: The '''Visual Protein Evidence''' and the '''Tabular Protein Evidence'''. == Visual Protein Evidence == === Location === '''Location''' stand for location of the product of the feature in the cell. This section presents output for tools that look for transmembrane helices (TM) or signal peptides (SP) in the feature. In the example, you can see five transmembrane helices in the protein identified by the Phobius tool. They are visualized as little boxes, and their location on the line depicts the location of the transmembrane helices in the protein. [[Image:EvidenceLocation.png]] === Domains === This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the whole length of the protein). Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]] in the menu bar. [[Image:EvidenceDomain.png]] === Similarities === [[Image:EvidenceSims1.png]] == Tabular Protein Evidence == === Similarities === === Domains === This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the whole length of the protein). The [[WebComponents/Table|table]] lists the '''Domain DB''' (the database for the domain that was hit), the '''ID''' in the domain database, the '''Name''' of the domain, the '''Location''' of the hit in the selected feature, the '''Score''' for the hit against the domain, as well as the '''Function''' of the domain. The table can be exported using the '''export table''' button. Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]] in the menu bar. [[Image:EvidenceDomTable.png]] === Identical Proteins === '''Essentially Identical Proteins''' are proteins that share a common sequence, but the start position of the proteins may vary a little. This definition was made because in different databases or close strains of organisms, it often happens that a protein is present, but the start position may be shifted in the finding genes step. So essentially, this table shows aliases of the feature that were based on protein identity. The first column of the [[WebComponents/Table|table]] shows the '''Database''' the alias can be found in, while the second column ('''ID''') offers the alias name and a link to the protein in the respective database. The following two columns describe the '''Organism''' and the '''Assignment''' for the feature for the alias. [[Image:EvidenceEIPs.png]] === Functionally Coupled === This [[WebComponent/Table|table]] lists all [[Glossary#Functional coupling|functionally coupled]] genes in the organism. You can see the '''Score''', the '''ID''' of the feature and the '''Function''' of the feature. [[Image:EvidenceFCs.png]] 6495400f244a90a7d40e7ea86580afc0dca7b34d 2059 2058 2008-11-25T10:14:27Z DanielaBartels 10 /* Similarities */ wikitext text/x-wiki The Evidence Page is divided into two parts via a [[WebComponents/Tabview|TabView]]: The '''Visual Protein Evidence''' and the '''Tabular Protein Evidence'''. == Visual Protein Evidence == === Location === '''Location''' stand for location of the product of the feature in the cell. This section presents output for tools that look for transmembrane helices (TM) or signal peptides (SP) in the feature. In the example, you can see five transmembrane helices in the protein identified by the Phobius tool. They are visualized as little boxes, and their location on the line depicts the location of the transmembrane helices in the protein. [[Image:EvidenceLocation.png]] === Domains === This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the whole length of the protein). Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]] in the menu bar. [[Image:EvidenceDomain.png]] === Similarities === [[Image:EvidenceSims1.png]] == Tabular Protein Evidence == === Similarities === [[Image:EvidenceFilter.png]] === Domains === This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the whole length of the protein). The [[WebComponents/Table|table]] lists the '''Domain DB''' (the database for the domain that was hit), the '''ID''' in the domain database, the '''Name''' of the domain, the '''Location''' of the hit in the selected feature, the '''Score''' for the hit against the domain, as well as the '''Function''' of the domain. The table can be exported using the '''export table''' button. Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]] in the menu bar. [[Image:EvidenceDomTable.png]] === Identical Proteins === '''Essentially Identical Proteins''' are proteins that share a common sequence, but the start position of the proteins may vary a little. This definition was made because in different databases or close strains of organisms, it often happens that a protein is present, but the start position may be shifted in the finding genes step. So essentially, this table shows aliases of the feature that were based on protein identity. The first column of the [[WebComponents/Table|table]] shows the '''Database''' the alias can be found in, while the second column ('''ID''') offers the alias name and a link to the protein in the respective database. The following two columns describe the '''Organism''' and the '''Assignment''' for the feature for the alias. [[Image:EvidenceEIPs.png]] === Functionally Coupled === This [[WebComponent/Table|table]] lists all [[Glossary#Functional coupling|functionally coupled]] genes in the organism. You can see the '''Score''', the '''ID''' of the feature and the '''Function''' of the feature. [[Image:EvidenceFCs.png]] d99d5ac9f4b0de235f3008707394658f0df4aaf8 2061 2059 2008-11-25T10:15:08Z DanielaBartels 10 /* Domains */ wikitext text/x-wiki The Evidence Page is divided into two parts via a [[WebComponents/Tabview|TabView]]: The '''Visual Protein Evidence''' and the '''Tabular Protein Evidence'''. == Visual Protein Evidence == === Location === '''Location''' stand for location of the product of the feature in the cell. This section presents output for tools that look for transmembrane helices (TM) or signal peptides (SP) in the feature. In the example, you can see five transmembrane helices in the protein identified by the Phobius tool. They are visualized as little boxes, and their location on the line depicts the location of the transmembrane helices in the protein. [[Image:EvidenceLocation.png]] === Domains === This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the whole length of the protein). Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]] in the menu bar. [[Image:EvidenceDomain.png]] === Similarities === [[Image:EvidenceSims1.png]] == Tabular Protein Evidence == === Similarities === [[Image:EvidenceFilter.png]] === Domains === This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the whole length of the protein). The [[WebComponents/Table|table]] lists the '''Domain DB''' (the database for the domain that was hit), the '''ID''' in the domain database, the '''Name''' of the domain, the '''Location''' of the hit in the selected feature, the '''Score''' for the hit against the domain, as well as the '''Function''' of the domain. The table can be exported using the '''export table''' button. Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]]''' in the menu bar. [[Image:EvidenceDomTable.png]] === Identical Proteins === '''Essentially Identical Proteins''' are proteins that share a common sequence, but the start position of the proteins may vary a little. This definition was made because in different databases or close strains of organisms, it often happens that a protein is present, but the start position may be shifted in the finding genes step. So essentially, this table shows aliases of the feature that were based on protein identity. The first column of the [[WebComponents/Table|table]] shows the '''Database''' the alias can be found in, while the second column ('''ID''') offers the alias name and a link to the protein in the respective database. The following two columns describe the '''Organism''' and the '''Assignment''' for the feature for the alias. [[Image:EvidenceEIPs.png]] === Functionally Coupled === This [[WebComponent/Table|table]] lists all [[Glossary#Functional coupling|functionally coupled]] genes in the organism. You can see the '''Score''', the '''ID''' of the feature and the '''Function''' of the feature. [[Image:EvidenceFCs.png]] e48d1ea44f88bc2f933d44bddfbdd8e06e4dff39 2062 2061 2008-11-25T10:17:56Z DanielaBartels 10 /* Domains */ wikitext text/x-wiki The Evidence Page is divided into two parts via a [[WebComponents/Tabview|TabView]]: The '''Visual Protein Evidence''' and the '''Tabular Protein Evidence'''. == Visual Protein Evidence == === Location === '''Location''' stand for location of the product of the feature in the cell. This section presents output for tools that look for transmembrane helices (TM) or signal peptides (SP) in the feature. In the example, you can see five transmembrane helices in the protein identified by the Phobius tool. They are visualized as little boxes, and their location on the line depicts the location of the transmembrane helices in the protein. [[Image:EvidenceLocation.png]] === Domains === This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the whole length of the protein). Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]]''' in the menu bar. [[Image:EvidenceDomain.png]] === Similarities === [[Image:EvidenceSims1.png]] == Tabular Protein Evidence == === Similarities === [[Image:EvidenceFilter.png]] === Domains === This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the whole length of the protein). The [[WebComponents/Table|table]] lists the '''Domain DB''' (the database for the domain that was hit), the '''ID''' in the domain database, the '''Name''' of the domain, the '''Location''' of the hit in the selected feature, the '''Score''' for the hit against the domain, as well as the '''Function''' of the domain. The table can be exported using the '''export table''' button. Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]]''' in the menu bar. [[Image:EvidenceDomTable.png]] === Identical Proteins === '''Essentially Identical Proteins''' are proteins that share a common sequence, but the start position of the proteins may vary a little. This definition was made because in different databases or close strains of organisms, it often happens that a protein is present, but the start position may be shifted in the finding genes step. So essentially, this table shows aliases of the feature that were based on protein identity. The first column of the [[WebComponents/Table|table]] shows the '''Database''' the alias can be found in, while the second column ('''ID''') offers the alias name and a link to the protein in the respective database. The following two columns describe the '''Organism''' and the '''Assignment''' for the feature for the alias. [[Image:EvidenceEIPs.png]] === Functionally Coupled === This [[WebComponent/Table|table]] lists all [[Glossary#Functional coupling|functionally coupled]] genes in the organism. You can see the '''Score''', the '''ID''' of the feature and the '''Function''' of the feature. [[Image:EvidenceFCs.png]] 391e4b572c5845a9ec33c5a917f1f78a72556455 2063 2062 2008-11-25T10:18:24Z DanielaBartels 10 /* Location */ wikitext text/x-wiki The Evidence Page is divided into two parts via a [[WebComponents/Tabview|TabView]]: The '''Visual Protein Evidence''' and the '''Tabular Protein Evidence'''. == Visual Protein Evidence == === Location === '''Location''' stand for location of the product of the feature in the cell. This section presents output for tools that look for transmembrane helices (TM) or signal peptides (SP) in the feature. In the example, you can see five transmembrane helices in the protein identified via the Phobius tool. They are visualized as little boxes, and their location on the line depicts the location of the transmembrane helices in the protein. [[Image:EvidenceLocation.png]] === Domains === This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the whole length of the protein). Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]]''' in the menu bar. [[Image:EvidenceDomain.png]] === Similarities === [[Image:EvidenceSims1.png]] == Tabular Protein Evidence == === Similarities === [[Image:EvidenceFilter.png]] === Domains === This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the whole length of the protein). The [[WebComponents/Table|table]] lists the '''Domain DB''' (the database for the domain that was hit), the '''ID''' in the domain database, the '''Name''' of the domain, the '''Location''' of the hit in the selected feature, the '''Score''' for the hit against the domain, as well as the '''Function''' of the domain. The table can be exported using the '''export table''' button. Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]]''' in the menu bar. [[Image:EvidenceDomTable.png]] === Identical Proteins === '''Essentially Identical Proteins''' are proteins that share a common sequence, but the start position of the proteins may vary a little. This definition was made because in different databases or close strains of organisms, it often happens that a protein is present, but the start position may be shifted in the finding genes step. So essentially, this table shows aliases of the feature that were based on protein identity. The first column of the [[WebComponents/Table|table]] shows the '''Database''' the alias can be found in, while the second column ('''ID''') offers the alias name and a link to the protein in the respective database. The following two columns describe the '''Organism''' and the '''Assignment''' for the feature for the alias. [[Image:EvidenceEIPs.png]] === Functionally Coupled === This [[WebComponent/Table|table]] lists all [[Glossary#Functional coupling|functionally coupled]] genes in the organism. You can see the '''Score''', the '''ID''' of the feature and the '''Function''' of the feature. [[Image:EvidenceFCs.png]] 6a4a651d4924c00c2ce3bb7db247fdca4df2e2a2 2064 2063 2008-11-25T10:19:13Z DanielaBartels 10 /* Similarities */ wikitext text/x-wiki The Evidence Page is divided into two parts via a [[WebComponents/Tabview|TabView]]: The '''Visual Protein Evidence''' and the '''Tabular Protein Evidence'''. == Visual Protein Evidence == === Location === '''Location''' stand for location of the product of the feature in the cell. This section presents output for tools that look for transmembrane helices (TM) or signal peptides (SP) in the feature. In the example, you can see five transmembrane helices in the protein identified via the Phobius tool. They are visualized as little boxes, and their location on the line depicts the location of the transmembrane helices in the protein. [[Image:EvidenceLocation.png]] === Domains === This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the whole length of the protein). Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]]''' in the menu bar. [[Image:EvidenceDomain.png]] === Similarities === [[Image:EvidenceFil1.png]] [[Image:EvidenceSims1.png]] == Tabular Protein Evidence == === Similarities === [[Image:EvidenceFilter.png]] === Domains === This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the whole length of the protein). The [[WebComponents/Table|table]] lists the '''Domain DB''' (the database for the domain that was hit), the '''ID''' in the domain database, the '''Name''' of the domain, the '''Location''' of the hit in the selected feature, the '''Score''' for the hit against the domain, as well as the '''Function''' of the domain. The table can be exported using the '''export table''' button. Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]]''' in the menu bar. [[Image:EvidenceDomTable.png]] === Identical Proteins === '''Essentially Identical Proteins''' are proteins that share a common sequence, but the start position of the proteins may vary a little. This definition was made because in different databases or close strains of organisms, it often happens that a protein is present, but the start position may be shifted in the finding genes step. So essentially, this table shows aliases of the feature that were based on protein identity. The first column of the [[WebComponents/Table|table]] shows the '''Database''' the alias can be found in, while the second column ('''ID''') offers the alias name and a link to the protein in the respective database. The following two columns describe the '''Organism''' and the '''Assignment''' for the feature for the alias. [[Image:EvidenceEIPs.png]] === Functionally Coupled === This [[WebComponent/Table|table]] lists all [[Glossary#Functional coupling|functionally coupled]] genes in the organism. You can see the '''Score''', the '''ID''' of the feature and the '''Function''' of the feature. [[Image:EvidenceFCs.png]] 4cf624b4bcc0bd08fc7607c72836cc070c8156f1 2067 2064 2008-11-25T10:35:57Z DanielaBartels 10 /* Similarities */ wikitext text/x-wiki The Evidence Page is divided into two parts via a [[WebComponents/Tabview|TabView]]: The '''Visual Protein Evidence''' and the '''Tabular Protein Evidence'''. == Visual Protein Evidence == === Location === '''Location''' stand for location of the product of the feature in the cell. This section presents output for tools that look for transmembrane helices (TM) or signal peptides (SP) in the feature. In the example, you can see five transmembrane helices in the protein identified via the Phobius tool. They are visualized as little boxes, and their location on the line depicts the location of the transmembrane helices in the protein. [[Image:EvidenceLocation.png]] === Domains === This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the whole length of the protein). Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]]''' in the menu bar. [[Image:EvidenceDomain.png]] === Similarities === [[Image:EvidenceSims1.png]] [[Image:EvidenceFil1.png]] == Tabular Protein Evidence == === Similarities === [[Image:EvidenceFilter.png]] === Domains === This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the whole length of the protein). The [[WebComponents/Table|table]] lists the '''Domain DB''' (the database for the domain that was hit), the '''ID''' in the domain database, the '''Name''' of the domain, the '''Location''' of the hit in the selected feature, the '''Score''' for the hit against the domain, as well as the '''Function''' of the domain. The table can be exported using the '''export table''' button. Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]]''' in the menu bar. [[Image:EvidenceDomTable.png]] === Identical Proteins === '''Essentially Identical Proteins''' are proteins that share a common sequence, but the start position of the proteins may vary a little. This definition was made because in different databases or close strains of organisms, it often happens that a protein is present, but the start position may be shifted in the finding genes step. So essentially, this table shows aliases of the feature that were based on protein identity. The first column of the [[WebComponents/Table|table]] shows the '''Database''' the alias can be found in, while the second column ('''ID''') offers the alias name and a link to the protein in the respective database. The following two columns describe the '''Organism''' and the '''Assignment''' for the feature for the alias. [[Image:EvidenceEIPs.png]] === Functionally Coupled === This [[WebComponent/Table|table]] lists all [[Glossary#Functional coupling|functionally coupled]] genes in the organism. You can see the '''Score''', the '''ID''' of the feature and the '''Function''' of the feature. [[Image:EvidenceFCs.png]] 6611d7a25b862bcab7c053751b102413a3b827af 2068 2067 2008-11-25T10:39:37Z DanielaBartels 10 /* Visual Protein Evidence */ wikitext text/x-wiki The Evidence Page is divided into two parts via a [[WebComponents/Tabview|TabView]]: The '''Visual Protein Evidence''' and the '''Tabular Protein Evidence'''. == Visual Protein Evidence == After loading the Evidence Page, the first tab of the [[WebComponent/Tabview|TabView]] is selected. It visually shows different pre-computed tool results for the given feature. In this view, you can see evidence for ''Location'' of the product of the gene in the cell, evidence for protein ''Domains'' and evidence that show ''Similarities'' to other features. === Location === '''Location''' stand for location of the product of the feature in the cell. This section presents output for tools that look for transmembrane helices (TM) or signal peptides (SP) in the feature. In the example, you can see five transmembrane helices in the protein identified via the Phobius tool. They are visualized as little boxes, and their location on the line depicts the location of the transmembrane helices in the protein. [[Image:EvidenceLocation.png]] === Domains === This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the whole length of the protein). Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]]''' in the menu bar. [[Image:EvidenceDomain.png]] === Similarities === [[Image:EvidenceSims1.png]] [[Image:EvidenceFil1.png]] == Tabular Protein Evidence == === Similarities === [[Image:EvidenceFilter.png]] === Domains === This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the whole length of the protein). The [[WebComponents/Table|table]] lists the '''Domain DB''' (the database for the domain that was hit), the '''ID''' in the domain database, the '''Name''' of the domain, the '''Location''' of the hit in the selected feature, the '''Score''' for the hit against the domain, as well as the '''Function''' of the domain. The table can be exported using the '''export table''' button. Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]]''' in the menu bar. [[Image:EvidenceDomTable.png]] === Identical Proteins === '''Essentially Identical Proteins''' are proteins that share a common sequence, but the start position of the proteins may vary a little. This definition was made because in different databases or close strains of organisms, it often happens that a protein is present, but the start position may be shifted in the finding genes step. So essentially, this table shows aliases of the feature that were based on protein identity. The first column of the [[WebComponents/Table|table]] shows the '''Database''' the alias can be found in, while the second column ('''ID''') offers the alias name and a link to the protein in the respective database. The following two columns describe the '''Organism''' and the '''Assignment''' for the feature for the alias. [[Image:EvidenceEIPs.png]] === Functionally Coupled === This [[WebComponent/Table|table]] lists all [[Glossary#Functional coupling|functionally coupled]] genes in the organism. You can see the '''Score''', the '''ID''' of the feature and the '''Function''' of the feature. [[Image:EvidenceFCs.png]] 097245b74ce3d35834885e3af17afe44c35e3593 2069 2068 2008-11-25T10:43:04Z DanielaBartels 10 /* Similarities */ wikitext text/x-wiki The Evidence Page is divided into two parts via a [[WebComponents/Tabview|TabView]]: The '''Visual Protein Evidence''' and the '''Tabular Protein Evidence'''. == Visual Protein Evidence == After loading the Evidence Page, the first tab of the [[WebComponent/Tabview|TabView]] is selected. It visually shows different pre-computed tool results for the given feature. In this view, you can see evidence for ''Location'' of the product of the gene in the cell, evidence for protein ''Domains'' and evidence that show ''Similarities'' to other features. === Location === '''Location''' stand for location of the product of the feature in the cell. This section presents output for tools that look for transmembrane helices (TM) or signal peptides (SP) in the feature. In the example, you can see five transmembrane helices in the protein identified via the Phobius tool. They are visualized as little boxes, and their location on the line depicts the location of the transmembrane helices in the protein. [[Image:EvidenceLocation.png]] === Domains === This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the whole length of the protein). Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]]''' in the menu bar. [[Image:EvidenceDomain.png]] === Similarities === This section graphically lists evidence for similarities to other features in the SEED database (or also other databases). The '''E-Value Key''' shown on the top defines the colors that are used to display different E-Value ranges for the similarities to the hit features. Hovering over the E-Value Key shows the value range for each color. [[Image:EvidenceSims1.png]] [[Image:EvidenceFil1.png]] == Tabular Protein Evidence == === Similarities === [[Image:EvidenceFilter.png]] === Domains === This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the whole length of the protein). The [[WebComponents/Table|table]] lists the '''Domain DB''' (the database for the domain that was hit), the '''ID''' in the domain database, the '''Name''' of the domain, the '''Location''' of the hit in the selected feature, the '''Score''' for the hit against the domain, as well as the '''Function''' of the domain. The table can be exported using the '''export table''' button. Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]]''' in the menu bar. [[Image:EvidenceDomTable.png]] === Identical Proteins === '''Essentially Identical Proteins''' are proteins that share a common sequence, but the start position of the proteins may vary a little. This definition was made because in different databases or close strains of organisms, it often happens that a protein is present, but the start position may be shifted in the finding genes step. So essentially, this table shows aliases of the feature that were based on protein identity. The first column of the [[WebComponents/Table|table]] shows the '''Database''' the alias can be found in, while the second column ('''ID''') offers the alias name and a link to the protein in the respective database. The following two columns describe the '''Organism''' and the '''Assignment''' for the feature for the alias. [[Image:EvidenceEIPs.png]] === Functionally Coupled === This [[WebComponent/Table|table]] lists all [[Glossary#Functional coupling|functionally coupled]] genes in the organism. You can see the '''Score''', the '''ID''' of the feature and the '''Function''' of the feature. [[Image:EvidenceFCs.png]] 7f54133b98e85d4a38e1416481dbeb34369eda94 2070 2069 2008-11-25T10:52:16Z DanielaBartels 10 /* Similarities */ wikitext text/x-wiki The Evidence Page is divided into two parts via a [[WebComponents/Tabview|TabView]]: The '''Visual Protein Evidence''' and the '''Tabular Protein Evidence'''. == Visual Protein Evidence == After loading the Evidence Page, the first tab of the [[WebComponent/Tabview|TabView]] is selected. It visually shows different pre-computed tool results for the given feature. In this view, you can see evidence for ''Location'' of the product of the gene in the cell, evidence for protein ''Domains'' and evidence that show ''Similarities'' to other features. === Location === '''Location''' stand for location of the product of the feature in the cell. This section presents output for tools that look for transmembrane helices (TM) or signal peptides (SP) in the feature. In the example, you can see five transmembrane helices in the protein identified via the Phobius tool. They are visualized as little boxes, and their location on the line depicts the location of the transmembrane helices in the protein. [[Image:EvidenceLocation.png]] === Domains === This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the whole length of the protein). Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]]''' in the menu bar. [[Image:EvidenceDomain.png]] === Similarities === This section graphically lists evidence for similarities to other features in the SEED database (or also other databases). The '''E-Value Key''' shown on the top defines the colors that are used to display different E-Value ranges for the similarities to the hit features. Hovering over the E-Value Key shows the value range for each color. Each similarity is represented by two bars, showing the alignment of the similarity. The first bar is the ''query'' feature, the second the ''hit'' feature. The length of the outside box shows the complete length of the respective sequence. The color of the outside box represents the range of the evalue score according to the E-Value Key bar. The length of the inner (white) box depicts the actual section of the sequence the similarity to the other feature is in. [[Image:EvidenceSims1.png]] [[Image:EvidenceFil1.png]] == Tabular Protein Evidence == === Similarities === [[Image:EvidenceFilter.png]] === Domains === This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the whole length of the protein). The [[WebComponents/Table|table]] lists the '''Domain DB''' (the database for the domain that was hit), the '''ID''' in the domain database, the '''Name''' of the domain, the '''Location''' of the hit in the selected feature, the '''Score''' for the hit against the domain, as well as the '''Function''' of the domain. The table can be exported using the '''export table''' button. Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]]''' in the menu bar. [[Image:EvidenceDomTable.png]] === Identical Proteins === '''Essentially Identical Proteins''' are proteins that share a common sequence, but the start position of the proteins may vary a little. This definition was made because in different databases or close strains of organisms, it often happens that a protein is present, but the start position may be shifted in the finding genes step. So essentially, this table shows aliases of the feature that were based on protein identity. The first column of the [[WebComponents/Table|table]] shows the '''Database''' the alias can be found in, while the second column ('''ID''') offers the alias name and a link to the protein in the respective database. The following two columns describe the '''Organism''' and the '''Assignment''' for the feature for the alias. [[Image:EvidenceEIPs.png]] === Functionally Coupled === This [[WebComponent/Table|table]] lists all [[Glossary#Functional coupling|functionally coupled]] genes in the organism. You can see the '''Score''', the '''ID''' of the feature and the '''Function''' of the feature. [[Image:EvidenceFCs.png]] 74f7a03c1b9c4e1c320292916c44c7abd0cbab63 2071 2070 2008-11-25T10:55:00Z DanielaBartels 10 /* Similarities */ wikitext text/x-wiki The Evidence Page is divided into two parts via a [[WebComponents/Tabview|TabView]]: The '''Visual Protein Evidence''' and the '''Tabular Protein Evidence'''. == Visual Protein Evidence == After loading the Evidence Page, the first tab of the [[WebComponent/Tabview|TabView]] is selected. It visually shows different pre-computed tool results for the given feature. In this view, you can see evidence for ''Location'' of the product of the gene in the cell, evidence for protein ''Domains'' and evidence that show ''Similarities'' to other features. === Location === '''Location''' stand for location of the product of the feature in the cell. This section presents output for tools that look for transmembrane helices (TM) or signal peptides (SP) in the feature. In the example, you can see five transmembrane helices in the protein identified via the Phobius tool. They are visualized as little boxes, and their location on the line depicts the location of the transmembrane helices in the protein. [[Image:EvidenceLocation.png]] === Domains === This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the whole length of the protein). Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]]''' in the menu bar. [[Image:EvidenceDomain.png]] === Similarities === This section graphically lists evidence for similarities to other features in the SEED database (or also other databases). The '''E-Value Key''' shown on the top defines the colors that are used to display different E-Value ranges for the similarities to the hit features. Hovering over the E-Value Key shows the value range for each color. Each similarity is represented by two bars, showing the alignment of the similarity. The first bar is the ''query'' feature, the second the ''hit'' feature. The length of the outside box shows the complete length of the respective sequence. The color of the outside box represents the range of the evalue score according to the E-Value Key bar. The length of the inner (white) box depicts the actual section of the sequence the similarity to the other feature is in. [[Image:EvidenceSims1.png]] [[Image:EvidenceHoverSim.png]] [[Image:EvidenceFil1.png]] == Tabular Protein Evidence == === Similarities === [[Image:EvidenceFilter.png]] === Domains === This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the whole length of the protein). The [[WebComponents/Table|table]] lists the '''Domain DB''' (the database for the domain that was hit), the '''ID''' in the domain database, the '''Name''' of the domain, the '''Location''' of the hit in the selected feature, the '''Score''' for the hit against the domain, as well as the '''Function''' of the domain. The table can be exported using the '''export table''' button. Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]]''' in the menu bar. [[Image:EvidenceDomTable.png]] === Identical Proteins === '''Essentially Identical Proteins''' are proteins that share a common sequence, but the start position of the proteins may vary a little. This definition was made because in different databases or close strains of organisms, it often happens that a protein is present, but the start position may be shifted in the finding genes step. So essentially, this table shows aliases of the feature that were based on protein identity. The first column of the [[WebComponents/Table|table]] shows the '''Database''' the alias can be found in, while the second column ('''ID''') offers the alias name and a link to the protein in the respective database. The following two columns describe the '''Organism''' and the '''Assignment''' for the feature for the alias. [[Image:EvidenceEIPs.png]] === Functionally Coupled === This [[WebComponent/Table|table]] lists all [[Glossary#Functional coupling|functionally coupled]] genes in the organism. You can see the '''Score''', the '''ID''' of the feature and the '''Function''' of the feature. [[Image:EvidenceFCs.png]] 5d08b03be0e674ab4b815f47fd6cbfb81935aff1 2073 2071 2008-11-25T11:05:35Z DanielaBartels 10 /* Similarities */ wikitext text/x-wiki The Evidence Page is divided into two parts via a [[WebComponents/Tabview|TabView]]: The '''Visual Protein Evidence''' and the '''Tabular Protein Evidence'''. == Visual Protein Evidence == After loading the Evidence Page, the first tab of the [[WebComponent/Tabview|TabView]] is selected. It visually shows different pre-computed tool results for the given feature. In this view, you can see evidence for ''Location'' of the product of the gene in the cell, evidence for protein ''Domains'' and evidence that show ''Similarities'' to other features. === Location === '''Location''' stand for location of the product of the feature in the cell. This section presents output for tools that look for transmembrane helices (TM) or signal peptides (SP) in the feature. In the example, you can see five transmembrane helices in the protein identified via the Phobius tool. They are visualized as little boxes, and their location on the line depicts the location of the transmembrane helices in the protein. [[Image:EvidenceLocation.png]] === Domains === This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the whole length of the protein). Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]]''' in the menu bar. [[Image:EvidenceDomain.png]] === Similarities === This section graphically lists evidence for similarities to other features in the SEED database (or also other databases). The '''E-Value Key''' shown on the top defines the colors that are used to display different E-Value ranges for the similarities to the hit features. Hovering over the E-Value Key shows the value range for each color. Each similarity is represented by two bars, showing the alignment of the similarity. The first bar is the ''query'' feature, the second the ''hit'' feature. The abbreviation in front of this bar informs you about the organism the hit feature is in. Hover over the abbreviation to get the complete organism name. Behind the box you can find the function of the hit feature. The length of the outside box shows the complete length of the respective sequence. The color of the outside box represents the range of the evalue score according to the E-Value Key bar. The length of the inner (white) box depicts the actual section of the sequence the similarity to the other feature is in. [[Image:EvidenceSims1.png]] [[Image:EvidenceHoverSim.png]] [[Image:EvidenceFil1.png]] == Tabular Protein Evidence == === Similarities === [[Image:EvidenceFilter.png]] === Domains === This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the whole length of the protein). The [[WebComponents/Table|table]] lists the '''Domain DB''' (the database for the domain that was hit), the '''ID''' in the domain database, the '''Name''' of the domain, the '''Location''' of the hit in the selected feature, the '''Score''' for the hit against the domain, as well as the '''Function''' of the domain. The table can be exported using the '''export table''' button. Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]]''' in the menu bar. [[Image:EvidenceDomTable.png]] === Identical Proteins === '''Essentially Identical Proteins''' are proteins that share a common sequence, but the start position of the proteins may vary a little. This definition was made because in different databases or close strains of organisms, it often happens that a protein is present, but the start position may be shifted in the finding genes step. So essentially, this table shows aliases of the feature that were based on protein identity. The first column of the [[WebComponents/Table|table]] shows the '''Database''' the alias can be found in, while the second column ('''ID''') offers the alias name and a link to the protein in the respective database. The following two columns describe the '''Organism''' and the '''Assignment''' for the feature for the alias. [[Image:EvidenceEIPs.png]] === Functionally Coupled === This [[WebComponent/Table|table]] lists all [[Glossary#Functional coupling|functionally coupled]] genes in the organism. You can see the '''Score''', the '''ID''' of the feature and the '''Function''' of the feature. [[Image:EvidenceFCs.png]] 2ef0a3e3ea5af4194a11bb5d677e9a6f7b4ff8d9 2074 2073 2008-11-25T11:06:27Z DanielaBartels 10 /* Similarities */ wikitext text/x-wiki The Evidence Page is divided into two parts via a [[WebComponents/Tabview|TabView]]: The '''Visual Protein Evidence''' and the '''Tabular Protein Evidence'''. == Visual Protein Evidence == After loading the Evidence Page, the first tab of the [[WebComponent/Tabview|TabView]] is selected. It visually shows different pre-computed tool results for the given feature. In this view, you can see evidence for ''Location'' of the product of the gene in the cell, evidence for protein ''Domains'' and evidence that show ''Similarities'' to other features. === Location === '''Location''' stand for location of the product of the feature in the cell. This section presents output for tools that look for transmembrane helices (TM) or signal peptides (SP) in the feature. In the example, you can see five transmembrane helices in the protein identified via the Phobius tool. They are visualized as little boxes, and their location on the line depicts the location of the transmembrane helices in the protein. [[Image:EvidenceLocation.png]] === Domains === This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the whole length of the protein). Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]]''' in the menu bar. [[Image:EvidenceDomain.png]] === Similarities === This section graphically lists evidence for similarities to other features in the SEED database (or also other databases). The '''E-Value Key''' shown on the top defines the colors that are used to display different E-Value ranges for the similarities to the hit features. Hovering over the E-Value Key shows the value range for each color. Each similarity is represented by two bars, showing the alignment of the similarity. The first bar is the '''query''' feature, the second the '''hit''' feature. The abbreviation in front of this bar informs you about the organism the hit feature is in. Hover over the abbreviation to get the complete organism name. Behind the box you can find the function of the hit feature. The length of the outside box shows the complete length of the respective sequence. The color of the outside box represents the range of the evalue score according to the E-Value Key bar. The length of the inner (white) box depicts the actual section of the sequence the similarity to the other feature is in. [[Image:EvidenceSims1.png]] [[Image:EvidenceHoverSim.png]] [[Image:EvidenceFil1.png]] == Tabular Protein Evidence == === Similarities === [[Image:EvidenceFilter.png]] === Domains === This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the whole length of the protein). The [[WebComponents/Table|table]] lists the '''Domain DB''' (the database for the domain that was hit), the '''ID''' in the domain database, the '''Name''' of the domain, the '''Location''' of the hit in the selected feature, the '''Score''' for the hit against the domain, as well as the '''Function''' of the domain. The table can be exported using the '''export table''' button. Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]]''' in the menu bar. [[Image:EvidenceDomTable.png]] === Identical Proteins === '''Essentially Identical Proteins''' are proteins that share a common sequence, but the start position of the proteins may vary a little. This definition was made because in different databases or close strains of organisms, it often happens that a protein is present, but the start position may be shifted in the finding genes step. So essentially, this table shows aliases of the feature that were based on protein identity. The first column of the [[WebComponents/Table|table]] shows the '''Database''' the alias can be found in, while the second column ('''ID''') offers the alias name and a link to the protein in the respective database. The following two columns describe the '''Organism''' and the '''Assignment''' for the feature for the alias. [[Image:EvidenceEIPs.png]] === Functionally Coupled === This [[WebComponent/Table|table]] lists all [[Glossary#Functional coupling|functionally coupled]] genes in the organism. You can see the '''Score''', the '''ID''' of the feature and the '''Function''' of the feature. [[Image:EvidenceFCs.png]] ed7c7930b19f484c7f389b75b7a17d8f8b59b319 2075 2074 2008-11-25T11:11:22Z DanielaBartels 10 /* Similarities */ wikitext text/x-wiki The Evidence Page is divided into two parts via a [[WebComponents/Tabview|TabView]]: The '''Visual Protein Evidence''' and the '''Tabular Protein Evidence'''. == Visual Protein Evidence == After loading the Evidence Page, the first tab of the [[WebComponent/Tabview|TabView]] is selected. It visually shows different pre-computed tool results for the given feature. In this view, you can see evidence for ''Location'' of the product of the gene in the cell, evidence for protein ''Domains'' and evidence that show ''Similarities'' to other features. === Location === '''Location''' stand for location of the product of the feature in the cell. This section presents output for tools that look for transmembrane helices (TM) or signal peptides (SP) in the feature. In the example, you can see five transmembrane helices in the protein identified via the Phobius tool. They are visualized as little boxes, and their location on the line depicts the location of the transmembrane helices in the protein. [[Image:EvidenceLocation.png]] === Domains === This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the whole length of the protein). Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]]''' in the menu bar. [[Image:EvidenceDomain.png]] === Similarities === This section graphically lists evidence for similarities to other features in the SEED database (or also other databases). The '''E-Value Key''' shown on the top defines the colors that are used to display different E-Value ranges for the similarities to the hit features. Hovering over the E-Value Key shows the value range for each color. Each similarity is represented by two bars, showing the alignment of the similarity. The first bar is the '''query''' feature, the second the '''hit''' feature. The abbreviation in front of this bar informs you about the organism the hit feature is in. Hover over the abbreviation to get the complete organism name. Behind the box you can find the function of the hit feature. The length of the outside box shows the complete length of the respective sequence. The color of the outside box represents the range of the evalue score according to the E-Value Key bar. The length of the inner (white) box depicts the actual section of the sequence the similarity to the other feature is in. Hovering over the box will show you some information about the hit feature, including the [[Glossary#Functional role|functional role]], the [[Glossary#Subsystem|subsystems]] and some values describing the hit to the query protein. [[Image:EvidenceSims1.png]] [[Image:EvidenceHoverSim.png]] [[Image:EvidenceFil1.png]] == Tabular Protein Evidence == === Similarities === [[Image:EvidenceFilter.png]] === Domains === This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the whole length of the protein). The [[WebComponents/Table|table]] lists the '''Domain DB''' (the database for the domain that was hit), the '''ID''' in the domain database, the '''Name''' of the domain, the '''Location''' of the hit in the selected feature, the '''Score''' for the hit against the domain, as well as the '''Function''' of the domain. The table can be exported using the '''export table''' button. Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]]''' in the menu bar. [[Image:EvidenceDomTable.png]] === Identical Proteins === '''Essentially Identical Proteins''' are proteins that share a common sequence, but the start position of the proteins may vary a little. This definition was made because in different databases or close strains of organisms, it often happens that a protein is present, but the start position may be shifted in the finding genes step. So essentially, this table shows aliases of the feature that were based on protein identity. The first column of the [[WebComponents/Table|table]] shows the '''Database''' the alias can be found in, while the second column ('''ID''') offers the alias name and a link to the protein in the respective database. The following two columns describe the '''Organism''' and the '''Assignment''' for the feature for the alias. [[Image:EvidenceEIPs.png]] === Functionally Coupled === This [[WebComponent/Table|table]] lists all [[Glossary#Functional coupling|functionally coupled]] genes in the organism. You can see the '''Score''', the '''ID''' of the feature and the '''Function''' of the feature. [[Image:EvidenceFCs.png]] b6645fd1fcded651007bcebcbdd2176dffa1b936 2076 2075 2008-11-25T11:11:57Z DanielaBartels 10 /* Similarities */ wikitext text/x-wiki The Evidence Page is divided into two parts via a [[WebComponents/Tabview|TabView]]: The '''Visual Protein Evidence''' and the '''Tabular Protein Evidence'''. == Visual Protein Evidence == After loading the Evidence Page, the first tab of the [[WebComponent/Tabview|TabView]] is selected. It visually shows different pre-computed tool results for the given feature. In this view, you can see evidence for ''Location'' of the product of the gene in the cell, evidence for protein ''Domains'' and evidence that show ''Similarities'' to other features. === Location === '''Location''' stand for location of the product of the feature in the cell. This section presents output for tools that look for transmembrane helices (TM) or signal peptides (SP) in the feature. In the example, you can see five transmembrane helices in the protein identified via the Phobius tool. They are visualized as little boxes, and their location on the line depicts the location of the transmembrane helices in the protein. [[Image:EvidenceLocation.png]] === Domains === This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the whole length of the protein). Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]]''' in the menu bar. [[Image:EvidenceDomain.png]] === Similarities === This section graphically lists evidence for similarities to other features in the SEED database (or also other databases). The '''E-Value Key''' shown on the top defines the colors that are used to display different E-Value ranges for the similarities to the hit features. Hovering over the E-Value Key shows the value range for each color. Each similarity is represented by two bars, showing the alignment of the similarity. The first bar is the '''query''' feature, the second the '''hit''' feature. The abbreviation in front of this bar informs you about the organism the hit feature is in. Hover over the abbreviation to get the complete organism name. Behind the box you can find the function of the hit feature. The length of the outside box shows the complete length of the respective sequence. The color of the outside box represents the range of the evalue score according to the E-Value Key bar. The length of the inner (white) box depicts the actual section of the sequence the similarity to the other feature is in. Hovering over the box will show you some information about the hit feature (see tooltip graphics below), including the [[Glossary#Functional role|functional role]], the [[Glossary#Subsystem|subsystems]] and some values describing the hit area. [[Image:EvidenceSims1.png]] [[Image:EvidenceHoverSim.png]] [[Image:EvidenceFil1.png]] == Tabular Protein Evidence == === Similarities === [[Image:EvidenceFilter.png]] === Domains === This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the whole length of the protein). The [[WebComponents/Table|table]] lists the '''Domain DB''' (the database for the domain that was hit), the '''ID''' in the domain database, the '''Name''' of the domain, the '''Location''' of the hit in the selected feature, the '''Score''' for the hit against the domain, as well as the '''Function''' of the domain. The table can be exported using the '''export table''' button. Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]]''' in the menu bar. [[Image:EvidenceDomTable.png]] === Identical Proteins === '''Essentially Identical Proteins''' are proteins that share a common sequence, but the start position of the proteins may vary a little. This definition was made because in different databases or close strains of organisms, it often happens that a protein is present, but the start position may be shifted in the finding genes step. So essentially, this table shows aliases of the feature that were based on protein identity. The first column of the [[WebComponents/Table|table]] shows the '''Database''' the alias can be found in, while the second column ('''ID''') offers the alias name and a link to the protein in the respective database. The following two columns describe the '''Organism''' and the '''Assignment''' for the feature for the alias. [[Image:EvidenceEIPs.png]] === Functionally Coupled === This [[WebComponent/Table|table]] lists all [[Glossary#Functional coupling|functionally coupled]] genes in the organism. You can see the '''Score''', the '''ID''' of the feature and the '''Function''' of the feature. [[Image:EvidenceFCs.png]] 3192da297084567ff59d8cf74da519a109221fc7 2077 2076 2008-11-25T11:17:54Z DanielaBartels 10 /* Similarities */ wikitext text/x-wiki The Evidence Page is divided into two parts via a [[WebComponents/Tabview|TabView]]: The '''Visual Protein Evidence''' and the '''Tabular Protein Evidence'''. == Visual Protein Evidence == After loading the Evidence Page, the first tab of the [[WebComponent/Tabview|TabView]] is selected. It visually shows different pre-computed tool results for the given feature. In this view, you can see evidence for ''Location'' of the product of the gene in the cell, evidence for protein ''Domains'' and evidence that show ''Similarities'' to other features. === Location === '''Location''' stand for location of the product of the feature in the cell. This section presents output for tools that look for transmembrane helices (TM) or signal peptides (SP) in the feature. In the example, you can see five transmembrane helices in the protein identified via the Phobius tool. They are visualized as little boxes, and their location on the line depicts the location of the transmembrane helices in the protein. [[Image:EvidenceLocation.png]] === Domains === This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the whole length of the protein). Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]]''' in the menu bar. [[Image:EvidenceDomain.png]] === Similarities === This section graphically lists evidence for similarities to other features in the SEED database (or also other databases). The '''E-Value Key''' shown on the top defines the colors that are used to display different E-Value ranges for the similarities to the hit features. Hovering over the E-Value Key shows the value range for each color. Each similarity is represented by two bars, showing the alignment of the similarity. The first bar is the '''query''' feature, the second the '''hit''' feature. The abbreviation in front of this bar informs you about the organism the hit feature is in. Hover over the abbreviation to get the complete organism name. Behind the box you can find the function of the hit feature. The length of the outside box shows the complete length of the respective sequence. The color of the outside box represents the range of the evalue score according to the E-Value Key bar. The length of the inner (white) box depicts the actual section of the sequence the similarity to the other feature is in. Hovering over the box will show you some information about the hit feature (see tooltip graphics below), including the [[Glossary#Functional role|functional role]], the [[Glossary#Subsystem|subsystems]] and some values describing the hit area. If you check some of the checkboxes in front of the [[Glossary#Functional role|functional role]] descriptions of the hit genes, you can access two function via the buttons on top of the Similarity graphics. The button '''Align Selected''' leads to an [[SEED_Viewer_Manual/AlignSeqs|alignment page]] showing a TCoffee alignment for the selected features. '''FASTA Download Selected''' lets you download the selected sequences in aminoacid FASTA format. [[Image:EvidenceSims1.png]] [[Image:EvidenceHoverSim.png]] [[Image:EvidenceFil1.png]] == Tabular Protein Evidence == === Similarities === [[Image:EvidenceFilter.png]] === Domains === This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the whole length of the protein). The [[WebComponents/Table|table]] lists the '''Domain DB''' (the database for the domain that was hit), the '''ID''' in the domain database, the '''Name''' of the domain, the '''Location''' of the hit in the selected feature, the '''Score''' for the hit against the domain, as well as the '''Function''' of the domain. The table can be exported using the '''export table''' button. Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]]''' in the menu bar. [[Image:EvidenceDomTable.png]] === Identical Proteins === '''Essentially Identical Proteins''' are proteins that share a common sequence, but the start position of the proteins may vary a little. This definition was made because in different databases or close strains of organisms, it often happens that a protein is present, but the start position may be shifted in the finding genes step. So essentially, this table shows aliases of the feature that were based on protein identity. The first column of the [[WebComponents/Table|table]] shows the '''Database''' the alias can be found in, while the second column ('''ID''') offers the alias name and a link to the protein in the respective database. The following two columns describe the '''Organism''' and the '''Assignment''' for the feature for the alias. [[Image:EvidenceEIPs.png]] === Functionally Coupled === This [[WebComponent/Table|table]] lists all [[Glossary#Functional coupling|functionally coupled]] genes in the organism. You can see the '''Score''', the '''ID''' of the feature and the '''Function''' of the feature. [[Image:EvidenceFCs.png]] 696c456bcd3abff45e281b6b408d29493aecf441 6 1505 2033 2008-11-24T16:03:58Z DanielaBartels 10 wikitext text/x-wiki da39a3ee5e6b4b0d3255bfef95601890afd80709 6 1506 2035 2008-11-24T16:04:56Z DanielaBartels 10 wikitext text/x-wiki da39a3ee5e6b4b0d3255bfef95601890afd80709 6 1507 2041 2008-11-24T16:17:34Z DanielaBartels 10 wikitext text/x-wiki da39a3ee5e6b4b0d3255bfef95601890afd80709 6 1508 2045 2008-11-24T16:22:54Z DanielaBartels 10 wikitext text/x-wiki da39a3ee5e6b4b0d3255bfef95601890afd80709 6 1509 2049 2008-11-24T16:33:14Z DanielaBartels 10 wikitext text/x-wiki da39a3ee5e6b4b0d3255bfef95601890afd80709 6 1510 2052 2008-11-24T16:45:14Z DanielaBartels 10 wikitext text/x-wiki da39a3ee5e6b4b0d3255bfef95601890afd80709 6 1511 2054 2008-11-24T16:46:21Z DanielaBartels 10 wikitext text/x-wiki da39a3ee5e6b4b0d3255bfef95601890afd80709 6 1512 2060 2008-11-25T10:14:41Z DanielaBartels 10 wikitext text/x-wiki da39a3ee5e6b4b0d3255bfef95601890afd80709 6 1513 2065 2008-11-25T10:19:33Z DanielaBartels 10 wikitext text/x-wiki da39a3ee5e6b4b0d3255bfef95601890afd80709 6 1514 2066 2008-11-25T10:34:01Z DanielaBartels 10 wikitext text/x-wiki da39a3ee5e6b4b0d3255bfef95601890afd80709 6 1515 2072 2008-11-25T10:55:16Z DanielaBartels 10 wikitext text/x-wiki da39a3ee5e6b4b0d3255bfef95601890afd80709 0 1502 2078 2077 2008-11-25T11:19:52Z DanielaBartels 10 /* Similarities */ wikitext text/x-wiki The Evidence Page is divided into two parts via a [[WebComponents/Tabview|TabView]]: The '''Visual Protein Evidence''' and the '''Tabular Protein Evidence'''. == Visual Protein Evidence == After loading the Evidence Page, the first tab of the [[WebComponent/Tabview|TabView]] is selected. It visually shows different pre-computed tool results for the given feature. In this view, you can see evidence for ''Location'' of the product of the gene in the cell, evidence for protein ''Domains'' and evidence that show ''Similarities'' to other features. === Location === '''Location''' stand for location of the product of the feature in the cell. This section presents output for tools that look for transmembrane helices (TM) or signal peptides (SP) in the feature. In the example, you can see five transmembrane helices in the protein identified via the Phobius tool. They are visualized as little boxes, and their location on the line depicts the location of the transmembrane helices in the protein. [[Image:EvidenceLocation.png]] === Domains === This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the whole length of the protein). Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]]''' in the menu bar. [[Image:EvidenceDomain.png]] === Similarities === This section graphically lists evidence for similarities to other features in the SEED database (or also other databases). The '''E-Value Key''' shown on the top defines the colors that are used to display different E-Value ranges for the similarities to the hit features. Hovering over the E-Value Key shows the value range for each color. Each similarity is represented by two bars, showing the alignment of the similarity. The first bar is the '''query''' feature, the second the '''hit''' feature. The abbreviation in front of this bar informs you about the organism the hit feature is in. Hover over the abbreviation to get the complete organism name. Behind the box you can find the [[Glossary#Functional role|functional role]] of the hit feature. The length of the outside box shows the complete length of the respective sequence. The color of the outside box represents the range of the evalue score according to the E-Value Key bar. The length of the inner (white) box depicts the actual section of the sequence the similarity to the other feature is in. Hovering over the box will show you some information about the hit feature (see tooltip graphics below), including the [[Glossary#Functional role|functional role]], the [[Glossary#Subsystem|subsystems]] and some values describing the hit area. If you check some of the checkboxes in front of the [[Glossary#Functional role|functional role]] descriptions of the hit genes, you can access two function via the buttons on top of the Similarity graphics. The button '''Align Selected''' leads to an [[SEED_Viewer_Manual/AlignSeqs|alignment page]] showing a TCoffee alignment for the selected features. '''FASTA Download Selected''' lets you download the selected sequences in aminoacid FASTA format. [[Image:EvidenceSims1.png]] [[Image:EvidenceHoverSim.png]] [[Image:EvidenceFil1.png]] == Tabular Protein Evidence == === Similarities === [[Image:EvidenceFilter.png]] === Domains === This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the whole length of the protein). The [[WebComponents/Table|table]] lists the '''Domain DB''' (the database for the domain that was hit), the '''ID''' in the domain database, the '''Name''' of the domain, the '''Location''' of the hit in the selected feature, the '''Score''' for the hit against the domain, as well as the '''Function''' of the domain. The table can be exported using the '''export table''' button. Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]]''' in the menu bar. [[Image:EvidenceDomTable.png]] === Identical Proteins === '''Essentially Identical Proteins''' are proteins that share a common sequence, but the start position of the proteins may vary a little. This definition was made because in different databases or close strains of organisms, it often happens that a protein is present, but the start position may be shifted in the finding genes step. So essentially, this table shows aliases of the feature that were based on protein identity. The first column of the [[WebComponents/Table|table]] shows the '''Database''' the alias can be found in, while the second column ('''ID''') offers the alias name and a link to the protein in the respective database. The following two columns describe the '''Organism''' and the '''Assignment''' for the feature for the alias. [[Image:EvidenceEIPs.png]] === Functionally Coupled === This [[WebComponent/Table|table]] lists all [[Glossary#Functional coupling|functionally coupled]] genes in the organism. You can see the '''Score''', the '''ID''' of the feature and the '''Function''' of the feature. [[Image:EvidenceFCs.png]] 81cdb19a13f5c53376b73b8c4aeddbcaafaf9329 2079 2078 2008-11-25T11:31:22Z DanielaBartels 10 /* Similarities */ wikitext text/x-wiki The Evidence Page is divided into two parts via a [[WebComponents/Tabview|TabView]]: The '''Visual Protein Evidence''' and the '''Tabular Protein Evidence'''. == Visual Protein Evidence == After loading the Evidence Page, the first tab of the [[WebComponent/Tabview|TabView]] is selected. It visually shows different pre-computed tool results for the given feature. In this view, you can see evidence for ''Location'' of the product of the gene in the cell, evidence for protein ''Domains'' and evidence that show ''Similarities'' to other features. === Location === '''Location''' stand for location of the product of the feature in the cell. This section presents output for tools that look for transmembrane helices (TM) or signal peptides (SP) in the feature. In the example, you can see five transmembrane helices in the protein identified via the Phobius tool. They are visualized as little boxes, and their location on the line depicts the location of the transmembrane helices in the protein. [[Image:EvidenceLocation.png]] === Domains === This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the whole length of the protein). Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]]''' in the menu bar. [[Image:EvidenceDomain.png]] === Similarities === This section graphically lists evidence for similarities to other features in the SEED database (or also other databases). The '''E-Value Key''' shown on the top defines the colors that are used to display different E-Value ranges for the similarities to the hit features. Hovering over the E-Value Key shows the value range for each color. Each similarity is represented by two bars, showing the alignment of the similarity. The first bar is the '''query''' feature, the second the '''hit''' feature. The abbreviation in front of this bar informs you about the organism the hit feature is in. Hover over the abbreviation to get the complete organism name. Behind the box you can find the [[Glossary#Functional role|functional role]] of the hit feature. The length of the outside box shows the complete length of the respective sequence. The color of the outside box represents the range of the evalue score according to the E-Value Key bar. The length of the inner (white) box depicts the actual section of the sequence the similarity to the other feature is in. Hovering over the box will show you some information about the hit feature (see tooltip graphics below), including the [[Glossary#Functional role|functional role]], the [[Glossary#Subsystem|subsystems]] and some values describing the hit area. If you check some of the checkboxes in front of the [[Glossary#Functional role|functional role]] descriptions of the hit genes, you can access two function via the buttons on top of the Similarity graphics. The button '''Align Selected''' leads to an [[SEED_Viewer_Manual/AlignSeqs|alignment page]] showing a TCoffee alignment for the selected features. '''FASTA Download Selected''' lets you download the selected sequences in aminoacid FASTA format. [[Image:EvidenceSims1.png]] [[Image:EvidenceHoverSim.png]] To change the evidence view with respect to the sorting and the filtering of the hits, you can find a little control box on top of the similarity graphics. '''Max Sims''' is the number of similarities that are listed on the page. '''Max E-Value''' filters out all similarities that have a higher E-Value than stated here. In the little combo box below these two values, you can decide to see only hits against the SEED database ('''Just FIG IDs'''), or also against other databases ('''Show all Databases'''). You can '''Sort''' the '''Results By''' ''Score'', ''Percent Identity'' (default) or ''Score per position''. [[Image:EvidenceFil1.png]] == Tabular Protein Evidence == === Similarities === [[Image:EvidenceFilter.png]] === Domains === This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the whole length of the protein). The [[WebComponents/Table|table]] lists the '''Domain DB''' (the database for the domain that was hit), the '''ID''' in the domain database, the '''Name''' of the domain, the '''Location''' of the hit in the selected feature, the '''Score''' for the hit against the domain, as well as the '''Function''' of the domain. The table can be exported using the '''export table''' button. Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]]''' in the menu bar. [[Image:EvidenceDomTable.png]] === Identical Proteins === '''Essentially Identical Proteins''' are proteins that share a common sequence, but the start position of the proteins may vary a little. This definition was made because in different databases or close strains of organisms, it often happens that a protein is present, but the start position may be shifted in the finding genes step. So essentially, this table shows aliases of the feature that were based on protein identity. The first column of the [[WebComponents/Table|table]] shows the '''Database''' the alias can be found in, while the second column ('''ID''') offers the alias name and a link to the protein in the respective database. The following two columns describe the '''Organism''' and the '''Assignment''' for the feature for the alias. [[Image:EvidenceEIPs.png]] === Functionally Coupled === This [[WebComponent/Table|table]] lists all [[Glossary#Functional coupling|functionally coupled]] genes in the organism. You can see the '''Score''', the '''ID''' of the feature and the '''Function''' of the feature. [[Image:EvidenceFCs.png]] 1661cc7a5c580f274c9ef8b78379949da8e6cad8 2080 2079 2008-11-25T11:33:05Z DanielaBartels 10 /* Similarities */ wikitext text/x-wiki The Evidence Page is divided into two parts via a [[WebComponents/Tabview|TabView]]: The '''Visual Protein Evidence''' and the '''Tabular Protein Evidence'''. == Visual Protein Evidence == After loading the Evidence Page, the first tab of the [[WebComponent/Tabview|TabView]] is selected. It visually shows different pre-computed tool results for the given feature. In this view, you can see evidence for ''Location'' of the product of the gene in the cell, evidence for protein ''Domains'' and evidence that show ''Similarities'' to other features. === Location === '''Location''' stand for location of the product of the feature in the cell. This section presents output for tools that look for transmembrane helices (TM) or signal peptides (SP) in the feature. In the example, you can see five transmembrane helices in the protein identified via the Phobius tool. They are visualized as little boxes, and their location on the line depicts the location of the transmembrane helices in the protein. [[Image:EvidenceLocation.png]] === Domains === This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the whole length of the protein). Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]]''' in the menu bar. [[Image:EvidenceDomain.png]] === Similarities === This section graphically lists evidence for similarities to other features in the SEED database (or also other databases). The '''E-Value Key''' shown on the top defines the colors that are used to display different E-Value ranges for the similarities to the hit features. Hovering over the E-Value Key shows the value range for each color. Each similarity is represented by two bars, showing the alignment of the similarity. The first bar is the '''query''' feature, the second the '''hit''' feature. The abbreviation in front of this bar informs you about the organism the hit feature is in. Hover over the abbreviation to get the complete organism name. Behind the box you can find the [[Glossary#Functional role|functional role]] of the hit feature. The length of the outside box shows the complete length of the respective sequence. The color of the outside box represents the range of the evalue score according to the E-Value Key bar. The length of the inner (white) box depicts the actual section of the sequence the similarity to the other feature is in. Hovering over the box will show you some information about the hit feature (see tooltip graphics below), including the [[Glossary#Functional role|functional role]], the [[Glossary#Subsystem|subsystems]] and some values describing the hit area. If you check some of the checkboxes in front of the [[Glossary#Functional role|functional role]] descriptions of the hit genes, you can access two function via the buttons on top of the Similarity graphics. The button '''Align Selected''' leads to an [[SEED_Viewer_Manual/AlignSeqs|alignment page]] showing a TCoffee alignment for the selected features. '''FASTA Download Selected''' lets you download the selected sequences in aminoacid FASTA format. [[Image:EvidenceSims1.png]] [[Image:EvidenceHoverSim.png]] To change the evidence view with respect to the sorting and the filtering of the hits, you can find a little control box on top of the similarity graphics. '''Max Sims''' is the number of similarities that are listed on the page. '''Max E-Value''' filters out all similarities that have a higher E-Value than stated here. In the little combo box below these two values, you can decide to see only hits against the SEED database ('''Just FIG IDs'''), or also against other databases ('''Show all Databases'''). You can '''Sort''' the '''Results By''' ''Score'', ''Percent Identity'' (default) or ''Score per position''. These values locally refer to the hit as known from BLAST hits, so a high percent identity referring to a very small hit region can make this similarity show up as one of the first hits, as shown in the example. [[Image:EvidenceFil1.png]] == Tabular Protein Evidence == === Similarities === [[Image:EvidenceFilter.png]] === Domains === This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the whole length of the protein). The [[WebComponents/Table|table]] lists the '''Domain DB''' (the database for the domain that was hit), the '''ID''' in the domain database, the '''Name''' of the domain, the '''Location''' of the hit in the selected feature, the '''Score''' for the hit against the domain, as well as the '''Function''' of the domain. The table can be exported using the '''export table''' button. Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]]''' in the menu bar. [[Image:EvidenceDomTable.png]] === Identical Proteins === '''Essentially Identical Proteins''' are proteins that share a common sequence, but the start position of the proteins may vary a little. This definition was made because in different databases or close strains of organisms, it often happens that a protein is present, but the start position may be shifted in the finding genes step. So essentially, this table shows aliases of the feature that were based on protein identity. The first column of the [[WebComponents/Table|table]] shows the '''Database''' the alias can be found in, while the second column ('''ID''') offers the alias name and a link to the protein in the respective database. The following two columns describe the '''Organism''' and the '''Assignment''' for the feature for the alias. [[Image:EvidenceEIPs.png]] === Functionally Coupled === This [[WebComponent/Table|table]] lists all [[Glossary#Functional coupling|functionally coupled]] genes in the organism. You can see the '''Score''', the '''ID''' of the feature and the '''Function''' of the feature. [[Image:EvidenceFCs.png]] 840445227b256b7f551f1f7bb716dc75a3b7a0b7 2081 2080 2008-11-25T11:46:57Z DanielaBartels 10 /* Similarities */ wikitext text/x-wiki The Evidence Page is divided into two parts via a [[WebComponents/Tabview|TabView]]: The '''Visual Protein Evidence''' and the '''Tabular Protein Evidence'''. == Visual Protein Evidence == After loading the Evidence Page, the first tab of the [[WebComponent/Tabview|TabView]] is selected. It visually shows different pre-computed tool results for the given feature. In this view, you can see evidence for ''Location'' of the product of the gene in the cell, evidence for protein ''Domains'' and evidence that show ''Similarities'' to other features. === Location === '''Location''' stand for location of the product of the feature in the cell. This section presents output for tools that look for transmembrane helices (TM) or signal peptides (SP) in the feature. In the example, you can see five transmembrane helices in the protein identified via the Phobius tool. They are visualized as little boxes, and their location on the line depicts the location of the transmembrane helices in the protein. [[Image:EvidenceLocation.png]] === Domains === This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the whole length of the protein). Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]]''' in the menu bar. [[Image:EvidenceDomain.png]] === Similarities === This section graphically lists evidence for similarities to other features in the SEED database (or also other databases). The '''E-Value Key''' shown on the top defines the colors that are used to display different E-Value ranges for the similarities to the hit features. Hovering over the E-Value Key shows the value range for each color. Each similarity is represented by two bars, showing the alignment of the similarity. The first bar is the '''query''' feature, the second the '''hit''' feature. The abbreviation in front of this bar informs you about the organism the hit feature is in. Hover over the abbreviation to get the complete organism name. Behind the box you can find the [[Glossary#Functional role|functional role]] of the hit feature. The length of the outside box shows the complete length of the respective sequence. The color of the outside box represents the range of the evalue score according to the E-Value Key bar. The length of the inner (white) box depicts the actual section of the sequence the similarity to the other feature is in. Hovering over the box will show you some information about the hit feature (see tooltip graphics below), including the [[Glossary#Functional role|functional role]], the [[Glossary#Subsystem|subsystems]] and some values describing the hit area. If you check some of the checkboxes in front of the [[Glossary#Functional role|functional role]] descriptions of the hit genes, you can access two function via the buttons on top of the Similarity graphics. The button '''Align Selected''' leads to an [[SEED_Viewer_Manual/AlignSeqs|alignment page]] showing a TCoffee alignment for the selected features. '''FASTA Download Selected''' lets you download the selected sequences in aminoacid FASTA format. [[Image:EvidenceSims1.png]] [[Image:EvidenceHoverSim.png]] To change the evidence view with respect to the sorting and the filtering of the hits, you can find a little control box on top of the similarity graphics. '''Max Sims''' is the number of similarities that are listed on the page. '''Max E-Value''' filters out all similarities that have a higher E-Value than stated here. In the little combo box below these two values, you can decide to see only hits against the SEED database ('''Just FIG IDs'''), or also against other databases ('''Show all Databases'''). You can '''Sort''' the '''Results By''' ''Score'', ''Percent Identity'' (default) or ''Score per position''. These values locally refer to the hit as known from BLAST hits, so a high percent identity referring to a very small hit region can make this similarity show up as one of the first hits, as shown in the example. [[Image:EvidenceFil1.png]] == Tabular Protein Evidence == === Similarities === [[Image:EvidenceSims2.png]] [[Image:EvidenceFilter.png]] === Domains === This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the whole length of the protein). The [[WebComponents/Table|table]] lists the '''Domain DB''' (the database for the domain that was hit), the '''ID''' in the domain database, the '''Name''' of the domain, the '''Location''' of the hit in the selected feature, the '''Score''' for the hit against the domain, as well as the '''Function''' of the domain. The table can be exported using the '''export table''' button. Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]]''' in the menu bar. [[Image:EvidenceDomTable.png]] === Identical Proteins === '''Essentially Identical Proteins''' are proteins that share a common sequence, but the start position of the proteins may vary a little. This definition was made because in different databases or close strains of organisms, it often happens that a protein is present, but the start position may be shifted in the finding genes step. So essentially, this table shows aliases of the feature that were based on protein identity. The first column of the [[WebComponents/Table|table]] shows the '''Database''' the alias can be found in, while the second column ('''ID''') offers the alias name and a link to the protein in the respective database. The following two columns describe the '''Organism''' and the '''Assignment''' for the feature for the alias. [[Image:EvidenceEIPs.png]] === Functionally Coupled === This [[WebComponent/Table|table]] lists all [[Glossary#Functional coupling|functionally coupled]] genes in the organism. You can see the '''Score''', the '''ID''' of the feature and the '''Function''' of the feature. [[Image:EvidenceFCs.png]] c7c6e6ac5251e6a3ef025c38d061dd0bfc9d74a1 2083 2081 2008-11-25T11:51:24Z DanielaBartels 10 /* Similarities */ wikitext text/x-wiki The Evidence Page is divided into two parts via a [[WebComponents/Tabview|TabView]]: The '''Visual Protein Evidence''' and the '''Tabular Protein Evidence'''. == Visual Protein Evidence == After loading the Evidence Page, the first tab of the [[WebComponent/Tabview|TabView]] is selected. It visually shows different pre-computed tool results for the given feature. In this view, you can see evidence for ''Location'' of the product of the gene in the cell, evidence for protein ''Domains'' and evidence that show ''Similarities'' to other features. === Location === '''Location''' stand for location of the product of the feature in the cell. This section presents output for tools that look for transmembrane helices (TM) or signal peptides (SP) in the feature. In the example, you can see five transmembrane helices in the protein identified via the Phobius tool. They are visualized as little boxes, and their location on the line depicts the location of the transmembrane helices in the protein. [[Image:EvidenceLocation.png]] === Domains === This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the whole length of the protein). Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]]''' in the menu bar. [[Image:EvidenceDomain.png]] === Similarities === This section graphically lists evidence for similarities to other features in the SEED database (or also other databases). The '''E-Value Key''' shown on the top defines the colors that are used to display different E-Value ranges for the similarities to the hit features. Hovering over the E-Value Key shows the value range for each color. Each similarity is represented by two bars, showing the alignment of the similarity. The first bar is the '''query''' feature, the second the '''hit''' feature. The abbreviation in front of this bar informs you about the organism the hit feature is in. Hover over the abbreviation to get the complete organism name. Behind the box you can find the [[Glossary#Functional role|functional role]] of the hit feature. The length of the outside box shows the complete length of the respective sequence. The color of the outside box represents the range of the evalue score according to the E-Value Key bar. The length of the inner (white) box depicts the actual section of the sequence the similarity to the other feature is in. Hovering over the box will show you some information about the hit feature (see tooltip graphics below), including the [[Glossary#Functional role|functional role]], the [[Glossary#Subsystem|subsystems]] and some values describing the hit area. If you check some of the checkboxes in front of the [[Glossary#Functional role|functional role]] descriptions of the hit genes, you can access two function via the buttons on top of the Similarity graphics. The button '''Align Selected''' leads to an [[SEED_Viewer_Manual/AlignSeqs|alignment page]] showing a TCoffee alignment for the selected features. '''FASTA Download Selected''' lets you download the selected sequences in aminoacid FASTA format. [[Image:EvidenceSims1.png]] [[Image:EvidenceHoverSim.png]] To change the evidence view with respect to the sorting and the filtering of the hits, you can find a little control box on top of the similarity graphics. '''Max Sims''' is the number of similarities that are listed on the page. '''Max E-Value''' filters out all similarities that have a higher E-Value than stated here. In the little combo box below these two values, you can decide to see only hits against the SEED database ('''Just FIG IDs'''), or also against other databases ('''Show all Databases'''). You can '''Sort''' the '''Results By''' ''Score'', ''Percent Identity'' (default) or ''Score per position''. These values locally refer to the hit as known from BLAST hits, so a high percent identity referring to a very small hit region can make this similarity show up as one of the first hits, as shown in the example. Checking '''Group by Genome''' will aggregate all hits to features in the same genome. A blue box will mark hits that belong to the same genome. After selecting the right values, you can press the button '''Resubmit''' to change the evidence view. [[Image:EvidenceFil1.png]] == Tabular Protein Evidence == === Similarities === [[Image:EvidenceSims2.png]] [[Image:EvidenceFilter.png]] === Domains === This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the whole length of the protein). The [[WebComponents/Table|table]] lists the '''Domain DB''' (the database for the domain that was hit), the '''ID''' in the domain database, the '''Name''' of the domain, the '''Location''' of the hit in the selected feature, the '''Score''' for the hit against the domain, as well as the '''Function''' of the domain. The table can be exported using the '''export table''' button. Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]]''' in the menu bar. [[Image:EvidenceDomTable.png]] === Identical Proteins === '''Essentially Identical Proteins''' are proteins that share a common sequence, but the start position of the proteins may vary a little. This definition was made because in different databases or close strains of organisms, it often happens that a protein is present, but the start position may be shifted in the finding genes step. So essentially, this table shows aliases of the feature that were based on protein identity. The first column of the [[WebComponents/Table|table]] shows the '''Database''' the alias can be found in, while the second column ('''ID''') offers the alias name and a link to the protein in the respective database. The following two columns describe the '''Organism''' and the '''Assignment''' for the feature for the alias. [[Image:EvidenceEIPs.png]] === Functionally Coupled === This [[WebComponent/Table|table]] lists all [[Glossary#Functional coupling|functionally coupled]] genes in the organism. You can see the '''Score''', the '''ID''' of the feature and the '''Function''' of the feature. [[Image:EvidenceFCs.png]] 5f7d647214eb5d5076fc1f3e61fec1b6f5c6b38a 2084 2083 2008-11-25T11:57:46Z DanielaBartels 10 /* Tabular Protein Evidence */ wikitext text/x-wiki The Evidence Page is divided into two parts via a [[WebComponents/Tabview|TabView]]: The '''Visual Protein Evidence''' and the '''Tabular Protein Evidence'''. == Visual Protein Evidence == After loading the Evidence Page, the first tab of the [[WebComponent/Tabview|TabView]] is selected. It visually shows different pre-computed tool results for the given feature. In this view, you can see evidence for ''Location'' of the product of the gene in the cell, evidence for protein ''Domains'' and evidence that show ''Similarities'' to other features. === Location === '''Location''' stand for location of the product of the feature in the cell. This section presents output for tools that look for transmembrane helices (TM) or signal peptides (SP) in the feature. In the example, you can see five transmembrane helices in the protein identified via the Phobius tool. They are visualized as little boxes, and their location on the line depicts the location of the transmembrane helices in the protein. [[Image:EvidenceLocation.png]] === Domains === This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the whole length of the protein). Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]]''' in the menu bar. [[Image:EvidenceDomain.png]] === Similarities === This section graphically lists evidence for similarities to other features in the SEED database (or also other databases). The '''E-Value Key''' shown on the top defines the colors that are used to display different E-Value ranges for the similarities to the hit features. Hovering over the E-Value Key shows the value range for each color. Each similarity is represented by two bars, showing the alignment of the similarity. The first bar is the '''query''' feature, the second the '''hit''' feature. The abbreviation in front of this bar informs you about the organism the hit feature is in. Hover over the abbreviation to get the complete organism name. Behind the box you can find the [[Glossary#Functional role|functional role]] of the hit feature. The length of the outside box shows the complete length of the respective sequence. The color of the outside box represents the range of the evalue score according to the E-Value Key bar. The length of the inner (white) box depicts the actual section of the sequence the similarity to the other feature is in. Hovering over the box will show you some information about the hit feature (see tooltip graphics below), including the [[Glossary#Functional role|functional role]], the [[Glossary#Subsystem|subsystems]] and some values describing the hit area. If you check some of the checkboxes in front of the [[Glossary#Functional role|functional role]] descriptions of the hit genes, you can access two function via the buttons on top of the Similarity graphics. The button '''Align Selected''' leads to an [[SEED_Viewer_Manual/AlignSeqs|alignment page]] showing a TCoffee alignment for the selected features. '''FASTA Download Selected''' lets you download the selected sequences in aminoacid FASTA format. [[Image:EvidenceSims1.png]] [[Image:EvidenceHoverSim.png]] To change the evidence view with respect to the sorting and the filtering of the hits, you can find a little control box on top of the similarity graphics. '''Max Sims''' is the number of similarities that are listed on the page. '''Max E-Value''' filters out all similarities that have a higher E-Value than stated here. In the little combo box below these two values, you can decide to see only hits against the SEED database ('''Just FIG IDs'''), or also against other databases ('''Show all Databases'''). You can '''Sort''' the '''Results By''' ''Score'', ''Percent Identity'' (default) or ''Score per position''. These values locally refer to the hit as known from BLAST hits, so a high percent identity referring to a very small hit region can make this similarity show up as one of the first hits, as shown in the example. Checking '''Group by Genome''' will aggregate all hits to features in the same genome. A blue box will mark hits that belong to the same genome. After selecting the right values, you can press the button '''Resubmit''' to change the evidence view. [[Image:EvidenceFil1.png]] == Tabular Protein Evidence == Activate the second tab of the large page-spanning [[WebComponents/Tabview|TabView]] to see the tabular view of the evidence. You will find most of the information already shown in the visual view, presented differently and enriched with some additional information. Added are the '''Identical Proteins''' and the '''Functionally coupled''' sections, while '''Location''' information is not presented in this tab. === Similarities === [[Image:EvidenceSims2.png]] [[Image:EvidenceFilter.png]] === Domains === This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the whole length of the protein). The [[WebComponents/Table|table]] lists the '''Domain DB''' (the database for the domain that was hit), the '''ID''' in the domain database, the '''Name''' of the domain, the '''Location''' of the hit in the selected feature, the '''Score''' for the hit against the domain, as well as the '''Function''' of the domain. The table can be exported using the '''export table''' button. Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]]''' in the menu bar. [[Image:EvidenceDomTable.png]] === Identical Proteins === '''Essentially Identical Proteins''' are proteins that share a common sequence, but the start position of the proteins may vary a little. This definition was made because in different databases or close strains of organisms, it often happens that a protein is present, but the start position may be shifted in the finding genes step. So essentially, this table shows aliases of the feature that were based on protein identity. The first column of the [[WebComponents/Table|table]] shows the '''Database''' the alias can be found in, while the second column ('''ID''') offers the alias name and a link to the protein in the respective database. The following two columns describe the '''Organism''' and the '''Assignment''' for the feature for the alias. [[Image:EvidenceEIPs.png]] === Functionally Coupled === This [[WebComponent/Table|table]] lists all [[Glossary#Functional coupling|functionally coupled]] genes in the organism. You can see the '''Score''', the '''ID''' of the feature and the '''Function''' of the feature. [[Image:EvidenceFCs.png]] 2d59f916e8aba200f96c0d4eb0bc77584e1d4d0c 2085 2084 2008-11-25T12:09:18Z DanielaBartels 10 /* Similarities */ wikitext text/x-wiki The Evidence Page is divided into two parts via a [[WebComponents/Tabview|TabView]]: The '''Visual Protein Evidence''' and the '''Tabular Protein Evidence'''. == Visual Protein Evidence == After loading the Evidence Page, the first tab of the [[WebComponent/Tabview|TabView]] is selected. It visually shows different pre-computed tool results for the given feature. In this view, you can see evidence for ''Location'' of the product of the gene in the cell, evidence for protein ''Domains'' and evidence that show ''Similarities'' to other features. === Location === '''Location''' stand for location of the product of the feature in the cell. This section presents output for tools that look for transmembrane helices (TM) or signal peptides (SP) in the feature. In the example, you can see five transmembrane helices in the protein identified via the Phobius tool. They are visualized as little boxes, and their location on the line depicts the location of the transmembrane helices in the protein. [[Image:EvidenceLocation.png]] === Domains === This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the whole length of the protein). Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]]''' in the menu bar. [[Image:EvidenceDomain.png]] === Similarities === This section graphically lists evidence for similarities to other features in the SEED database (or also other databases). The '''E-Value Key''' shown on the top defines the colors that are used to display different E-Value ranges for the similarities to the hit features. Hovering over the E-Value Key shows the value range for each color. Each similarity is represented by two bars, showing the alignment of the similarity. The first bar is the '''query''' feature, the second the '''hit''' feature. The abbreviation in front of this bar informs you about the organism the hit feature is in. Hover over the abbreviation to get the complete organism name. Behind the box you can find the [[Glossary#Functional role|functional role]] of the hit feature. The length of the outside box shows the complete length of the respective sequence. The color of the outside box represents the range of the evalue score according to the E-Value Key bar. The length of the inner (white) box depicts the actual section of the sequence the similarity to the other feature is in. Hovering over the box will show you some information about the hit feature (see tooltip graphics below), including the [[Glossary#Functional role|functional role]], the [[Glossary#Subsystem|subsystems]] and some values describing the hit area. If you check some of the checkboxes in front of the [[Glossary#Functional role|functional role]] descriptions of the hit genes, you can access two function via the buttons on top of the Similarity graphics. The button '''Align Selected''' leads to an [[SEED_Viewer_Manual/AlignSeqs|alignment page]] showing a TCoffee alignment for the selected features. '''FASTA Download Selected''' lets you download the selected sequences in aminoacid FASTA format. [[Image:EvidenceSims1.png]] [[Image:EvidenceHoverSim.png]] To change the evidence view with respect to the sorting and the filtering of the hits, you can find a little control box on top of the similarity graphics. '''Max Sims''' is the number of similarities that are listed on the page. '''Max E-Value''' filters out all similarities that have a higher E-Value than stated here. In the little combo box below these two values, you can decide to see only hits against the SEED database ('''Just FIG IDs'''), or also against other databases ('''Show all Databases'''). You can '''Sort''' the '''Results By''' ''Score'', ''Percent Identity'' (default) or ''Score per position''. These values locally refer to the hit as known from BLAST hits, so a high percent identity referring to a very small hit region can make this similarity show up as one of the first hits, as shown in the example. Checking '''Group by Genome''' will aggregate all hits to features in the same genome. A blue box will mark hits that belong to the same genome. After selecting the right values, you can press the button '''Resubmit''' to change the evidence view. [[Image:EvidenceFil1.png]] == Tabular Protein Evidence == Activate the second tab of the large page-spanning [[WebComponents/Tabview|TabView]] to see the tabular view of the evidence. You will find most of the information already shown in the visual view, presented differently and enriched with some additional information. Added are the '''Identical Proteins''' and the '''Functionally coupled''' sections, while '''Location''' information is not presented in this tab. === Similarities === The similarity [[WebComponents/Table|table]] lists hits to similar features in the SEED database (or also other databases), like described for the [[SEED_Viewer_Manual/Visual Protein Evidence|Visual Protein Evidence]]. Each row in the table represents a hit. The first column provides a checkbox to select a hit feature. Again, the buttons '''Align Selected''' and '''FASTA Download Selected''' are present and can be used to get to a TCoffee [[SEED_Viewer_Manual/AlignSeqs|alignment page]] or download the protein sequences of the selected features in FASTA format. The two buttons in the column header allow mass selection of the features. '''All''' will select all features visible in the table. '''check to last checked''' lets you select all features up to a selected feature in the [[WebComponents/Table|table]]. Organism Color Help Organism cells are colored according to their taxonomy family. [?] Similar FIG Sequence E-value Percent Identity Region in Query peg Alignment Color Help Cell colors represent the amount and the region of similarity between the query and hit sequence. Click question mark for more information. [?] Region in Similar Sequence Alignment Color Help Cell colors represent the amount and the region of similarity between the query and hit sequence. Click question mark for more information. [?] Organism Organism Color Help Organism cells are colored according to their taxonomy family. [?] Function Function Color Help Colors in the function cell relate to similarity of function to the query sequence. Click question mark for color meaning. [?] Associated Subsystem Evidence Code Evidence Code Help The evidence code reflect significant factors that go into making assignments of function. Click question mark for more information. [[Image:EvidenceSims2.png]] [[Image:EvidenceFilter.png]] === Domains === This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the whole length of the protein). The [[WebComponents/Table|table]] lists the '''Domain DB''' (the database for the domain that was hit), the '''ID''' in the domain database, the '''Name''' of the domain, the '''Location''' of the hit in the selected feature, the '''Score''' for the hit against the domain, as well as the '''Function''' of the domain. The table can be exported using the '''export table''' button. Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]]''' in the menu bar. [[Image:EvidenceDomTable.png]] === Identical Proteins === '''Essentially Identical Proteins''' are proteins that share a common sequence, but the start position of the proteins may vary a little. This definition was made because in different databases or close strains of organisms, it often happens that a protein is present, but the start position may be shifted in the finding genes step. So essentially, this table shows aliases of the feature that were based on protein identity. The first column of the [[WebComponents/Table|table]] shows the '''Database''' the alias can be found in, while the second column ('''ID''') offers the alias name and a link to the protein in the respective database. The following two columns describe the '''Organism''' and the '''Assignment''' for the feature for the alias. [[Image:EvidenceEIPs.png]] === Functionally Coupled === This [[WebComponent/Table|table]] lists all [[Glossary#Functional coupling|functionally coupled]] genes in the organism. You can see the '''Score''', the '''ID''' of the feature and the '''Function''' of the feature. [[Image:EvidenceFCs.png]] 1616ee3df7650b8adf48e0e54dfb8de388e3c09a 2086 2085 2008-11-25T12:16:22Z DanielaBartels 10 /* Similarities */ wikitext text/x-wiki The Evidence Page is divided into two parts via a [[WebComponents/Tabview|TabView]]: The '''Visual Protein Evidence''' and the '''Tabular Protein Evidence'''. == Visual Protein Evidence == After loading the Evidence Page, the first tab of the [[WebComponent/Tabview|TabView]] is selected. It visually shows different pre-computed tool results for the given feature. In this view, you can see evidence for ''Location'' of the product of the gene in the cell, evidence for protein ''Domains'' and evidence that show ''Similarities'' to other features. === Location === '''Location''' stand for location of the product of the feature in the cell. This section presents output for tools that look for transmembrane helices (TM) or signal peptides (SP) in the feature. In the example, you can see five transmembrane helices in the protein identified via the Phobius tool. They are visualized as little boxes, and their location on the line depicts the location of the transmembrane helices in the protein. [[Image:EvidenceLocation.png]] === Domains === This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the whole length of the protein). Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]]''' in the menu bar. [[Image:EvidenceDomain.png]] === Similarities === This section graphically lists evidence for similarities to other features in the SEED database (or also other databases). The '''E-Value Key''' shown on the top defines the colors that are used to display different E-Value ranges for the similarities to the hit features. Hovering over the E-Value Key shows the value range for each color. Each similarity is represented by two bars, showing the alignment of the similarity. The first bar is the '''query''' feature, the second the '''hit''' feature. The abbreviation in front of this bar informs you about the organism the hit feature is in. Hover over the abbreviation to get the complete organism name. Behind the box you can find the [[Glossary#Functional role|functional role]] of the hit feature. The length of the outside box shows the complete length of the respective sequence. The color of the outside box represents the range of the evalue score according to the E-Value Key bar. The length of the inner (white) box depicts the actual section of the sequence the similarity to the other feature is in. Hovering over the box will show you some information about the hit feature (see tooltip graphics below), including the [[Glossary#Functional role|functional role]], the [[Glossary#Subsystem|subsystems]] and some values describing the hit area. If you check some of the checkboxes in front of the [[Glossary#Functional role|functional role]] descriptions of the hit genes, you can access two function via the buttons on top of the Similarity graphics. The button '''Align Selected''' leads to an [[SEED_Viewer_Manual/AlignSeqs|alignment page]] showing a TCoffee alignment for the selected features. '''FASTA Download Selected''' lets you download the selected sequences in aminoacid FASTA format. [[Image:EvidenceSims1.png]] [[Image:EvidenceHoverSim.png]] To change the evidence view with respect to the sorting and the filtering of the hits, you can find a little control box on top of the similarity graphics. '''Max Sims''' is the number of similarities that are listed on the page. '''Max E-Value''' filters out all similarities that have a higher E-Value than stated here. In the little combo box below these two values, you can decide to see only hits against the SEED database ('''Just FIG IDs'''), or also against other databases ('''Show all Databases'''). You can '''Sort''' the '''Results By''' ''Score'', ''Percent Identity'' (default) or ''Score per position''. These values locally refer to the hit as known from BLAST hits, so a high percent identity referring to a very small hit region can make this similarity show up as one of the first hits, as shown in the example. Checking '''Group by Genome''' will aggregate all hits to features in the same genome. A blue box will mark hits that belong to the same genome. After selecting the right values, you can press the button '''Resubmit''' to change the evidence view. [[Image:EvidenceFil1.png]] == Tabular Protein Evidence == Activate the second tab of the large page-spanning [[WebComponents/Tabview|TabView]] to see the tabular view of the evidence. You will find most of the information already shown in the visual view, presented differently and enriched with some additional information. Added are the '''Identical Proteins''' and the '''Functionally coupled''' sections, while '''Location''' information is not presented in this tab. === Similarities === The similarity [[WebComponents/Table|table]] lists hits to similar features in the SEED database (or also other databases), like described for the [[SEED_Viewer_Manual/Visual Protein Evidence|Visual Protein Evidence]]. Each row in the table represents a hit. The first column provides a checkbox to select a hit feature. Again, the buttons '''Align Selected''' and '''FASTA Download Selected''' are present and can be used to get to a TCoffee [[SEED_Viewer_Manual/AlignSeqs|alignment page]] or download the protein sequences of the selected features in FASTA format. The two buttons in the column header allow mass selection of the features. '''All''' will select all features visible in the table, '''check to last checked''' lets you select all features up to a selected feature in the [[WebComponents/Table|table]]. The ID of the hit features, as well as a link to the [[SEED_Viewer_Manual/Annotation|annotation page]] is displayed in the column '''Similar FIG Sequence'''. The next four columns describe information to the hit regions of the query and hit features ('''E-value''', '''Percent Identity''', '''Region in Query peg''' and '''Region in Similar Sequence'''). Cell colors represent the amount and the region of similarity between the query and hit sequence. Click question mark for more information. [?] Organism Organism Color Help Organism cells are colored according to their taxonomy family. [?] Function Function Color Help Colors in the function cell relate to similarity of function to the query sequence. Click question mark for color meaning. [?] Associated Subsystem Evidence Code Evidence Code Help The evidence code reflect significant factors that go into making assignments of function. Click question mark for more information. [[Image:EvidenceSims2.png]] [[Image:EvidenceFilter.png]] === Domains === This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the whole length of the protein). The [[WebComponents/Table|table]] lists the '''Domain DB''' (the database for the domain that was hit), the '''ID''' in the domain database, the '''Name''' of the domain, the '''Location''' of the hit in the selected feature, the '''Score''' for the hit against the domain, as well as the '''Function''' of the domain. The table can be exported using the '''export table''' button. Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]]''' in the menu bar. [[Image:EvidenceDomTable.png]] === Identical Proteins === '''Essentially Identical Proteins''' are proteins that share a common sequence, but the start position of the proteins may vary a little. This definition was made because in different databases or close strains of organisms, it often happens that a protein is present, but the start position may be shifted in the finding genes step. So essentially, this table shows aliases of the feature that were based on protein identity. The first column of the [[WebComponents/Table|table]] shows the '''Database''' the alias can be found in, while the second column ('''ID''') offers the alias name and a link to the protein in the respective database. The following two columns describe the '''Organism''' and the '''Assignment''' for the feature for the alias. [[Image:EvidenceEIPs.png]] === Functionally Coupled === This [[WebComponent/Table|table]] lists all [[Glossary#Functional coupling|functionally coupled]] genes in the organism. You can see the '''Score''', the '''ID''' of the feature and the '''Function''' of the feature. [[Image:EvidenceFCs.png]] 16aca10cb8a673fe0618848e833201a282218449 2087 2086 2008-11-25T12:18:49Z DanielaBartels 10 /* Similarities */ wikitext text/x-wiki The Evidence Page is divided into two parts via a [[WebComponents/Tabview|TabView]]: The '''Visual Protein Evidence''' and the '''Tabular Protein Evidence'''. == Visual Protein Evidence == After loading the Evidence Page, the first tab of the [[WebComponent/Tabview|TabView]] is selected. It visually shows different pre-computed tool results for the given feature. In this view, you can see evidence for ''Location'' of the product of the gene in the cell, evidence for protein ''Domains'' and evidence that show ''Similarities'' to other features. === Location === '''Location''' stand for location of the product of the feature in the cell. This section presents output for tools that look for transmembrane helices (TM) or signal peptides (SP) in the feature. In the example, you can see five transmembrane helices in the protein identified via the Phobius tool. They are visualized as little boxes, and their location on the line depicts the location of the transmembrane helices in the protein. [[Image:EvidenceLocation.png]] === Domains === This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the whole length of the protein). Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]]''' in the menu bar. [[Image:EvidenceDomain.png]] === Similarities === This section graphically lists evidence for similarities to other features in the SEED database (or also other databases). The '''E-Value Key''' shown on the top defines the colors that are used to display different E-Value ranges for the similarities to the hit features. Hovering over the E-Value Key shows the value range for each color. Each similarity is represented by two bars, showing the alignment of the similarity. The first bar is the '''query''' feature, the second the '''hit''' feature. The abbreviation in front of this bar informs you about the organism the hit feature is in. Hover over the abbreviation to get the complete organism name. Behind the box you can find the [[Glossary#Functional role|functional role]] of the hit feature. The length of the outside box shows the complete length of the respective sequence. The color of the outside box represents the range of the evalue score according to the E-Value Key bar. The length of the inner (white) box depicts the actual section of the sequence the similarity to the other feature is in. Hovering over the box will show you some information about the hit feature (see tooltip graphics below), including the [[Glossary#Functional role|functional role]], the [[Glossary#Subsystem|subsystems]] and some values describing the hit area. If you check some of the checkboxes in front of the [[Glossary#Functional role|functional role]] descriptions of the hit genes, you can access two function via the buttons on top of the Similarity graphics. The button '''Align Selected''' leads to an [[SEED_Viewer_Manual/AlignSeqs|alignment page]] showing a TCoffee alignment for the selected features. '''FASTA Download Selected''' lets you download the selected sequences in aminoacid FASTA format. [[Image:EvidenceSims1.png]] [[Image:EvidenceHoverSim.png]] To change the evidence view with respect to the sorting and the filtering of the hits, you can find a little control box on top of the similarity graphics. '''Max Sims''' is the number of similarities that are listed on the page. '''Max E-Value''' filters out all similarities that have a higher E-Value than stated here. In the little combo box below these two values, you can decide to see only hits against the SEED database ('''Just FIG IDs'''), or also against other databases ('''Show all Databases'''). You can '''Sort''' the '''Results By''' ''Score'', ''Percent Identity'' (default) or ''Score per position''. These values locally refer to the hit as known from BLAST hits, so a high percent identity referring to a very small hit region can make this similarity show up as one of the first hits, as shown in the example. Checking '''Group by Genome''' will aggregate all hits to features in the same genome. A blue box will mark hits that belong to the same genome. After selecting the right values, you can press the button '''Resubmit''' to change the evidence view. [[Image:EvidenceFil1.png]] == Tabular Protein Evidence == Activate the second tab of the large page-spanning [[WebComponents/Tabview|TabView]] to see the tabular view of the evidence. You will find most of the information already shown in the visual view, presented differently and enriched with some additional information. Added are the '''Identical Proteins''' and the '''Functionally coupled''' sections, while '''Location''' information is not presented in this tab. === Similarities === The similarity [[WebComponents/Table|table]] lists hits to similar features in the SEED database (or also other databases), like described for the [[SEED_Viewer_Manual/Visual Protein Evidence|Visual Protein Evidence]]. Each row in the table represents a hit. The first column provides a checkbox to select a hit feature. Again, the buttons '''Align Selected''' and '''FASTA Download Selected''' are present and can be used to get to a TCoffee [[SEED_Viewer_Manual/AlignSeqs|alignment page]] or download the protein sequences of the selected features in FASTA format. The two buttons in the column header allow mass selection of the features. '''All''' will select all features visible in the table, '''check to last checked''' lets you select all features up to a selected feature in the [[WebComponents/Table|table]]. The ID of the hit features, as well as a link to the [[SEED_Viewer_Manual/Annotation|annotation page]] is displayed in the column '''Similar FIG Sequence'''. The next four columns describe information to the hit regions of the query and hit features ('''E-value''', '''Percent Identity''', '''Region in Query peg''' and '''Region in Similar Sequence'''). Organism Function Associated Subsystem Evidence Code [[Image:EvidenceSims2.png]] [[Image:EvidenceFilter.png]] === Domains === This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the whole length of the protein). The [[WebComponents/Table|table]] lists the '''Domain DB''' (the database for the domain that was hit), the '''ID''' in the domain database, the '''Name''' of the domain, the '''Location''' of the hit in the selected feature, the '''Score''' for the hit against the domain, as well as the '''Function''' of the domain. The table can be exported using the '''export table''' button. Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]]''' in the menu bar. [[Image:EvidenceDomTable.png]] === Identical Proteins === '''Essentially Identical Proteins''' are proteins that share a common sequence, but the start position of the proteins may vary a little. This definition was made because in different databases or close strains of organisms, it often happens that a protein is present, but the start position may be shifted in the finding genes step. So essentially, this table shows aliases of the feature that were based on protein identity. The first column of the [[WebComponents/Table|table]] shows the '''Database''' the alias can be found in, while the second column ('''ID''') offers the alias name and a link to the protein in the respective database. The following two columns describe the '''Organism''' and the '''Assignment''' for the feature for the alias. [[Image:EvidenceEIPs.png]] === Functionally Coupled === This [[WebComponent/Table|table]] lists all [[Glossary#Functional coupling|functionally coupled]] genes in the organism. You can see the '''Score''', the '''ID''' of the feature and the '''Function''' of the feature. [[Image:EvidenceFCs.png]] efa4cd5f91bb5577c97cb5981860a7d90738ed84 2088 2087 2008-11-25T12:25:20Z DanielaBartels 10 /* Similarities */ wikitext text/x-wiki The Evidence Page is divided into two parts via a [[WebComponents/Tabview|TabView]]: The '''Visual Protein Evidence''' and the '''Tabular Protein Evidence'''. == Visual Protein Evidence == After loading the Evidence Page, the first tab of the [[WebComponent/Tabview|TabView]] is selected. It visually shows different pre-computed tool results for the given feature. In this view, you can see evidence for ''Location'' of the product of the gene in the cell, evidence for protein ''Domains'' and evidence that show ''Similarities'' to other features. === Location === '''Location''' stand for location of the product of the feature in the cell. This section presents output for tools that look for transmembrane helices (TM) or signal peptides (SP) in the feature. In the example, you can see five transmembrane helices in the protein identified via the Phobius tool. They are visualized as little boxes, and their location on the line depicts the location of the transmembrane helices in the protein. [[Image:EvidenceLocation.png]] === Domains === This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the whole length of the protein). Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]]''' in the menu bar. [[Image:EvidenceDomain.png]] === Similarities === This section graphically lists evidence for similarities to other features in the SEED database (or also other databases). The '''E-Value Key''' shown on the top defines the colors that are used to display different E-Value ranges for the similarities to the hit features. Hovering over the E-Value Key shows the value range for each color. Each similarity is represented by two bars, showing the alignment of the similarity. The first bar is the '''query''' feature, the second the '''hit''' feature. The abbreviation in front of this bar informs you about the organism the hit feature is in. Hover over the abbreviation to get the complete organism name. Behind the box you can find the [[Glossary#Functional role|functional role]] of the hit feature. The length of the outside box shows the complete length of the respective sequence. The color of the outside box represents the range of the evalue score according to the E-Value Key bar. The length of the inner (white) box depicts the actual section of the sequence the similarity to the other feature is in. Hovering over the box will show you some information about the hit feature (see tooltip graphics below), including the [[Glossary#Functional role|functional role]], the [[Glossary#Subsystem|subsystems]] and some values describing the hit area. If you check some of the checkboxes in front of the [[Glossary#Functional role|functional role]] descriptions of the hit genes, you can access two function via the buttons on top of the Similarity graphics. The button '''Align Selected''' leads to an [[SEED_Viewer_Manual/AlignSeqs|alignment page]] showing a TCoffee alignment for the selected features. '''FASTA Download Selected''' lets you download the selected sequences in aminoacid FASTA format. [[Image:EvidenceSims1.png]] [[Image:EvidenceHoverSim.png]] To change the evidence view with respect to the sorting and the filtering of the hits, you can find a little control box on top of the similarity graphics. '''Max Sims''' is the number of similarities that are listed on the page. '''Max E-Value''' filters out all similarities that have a higher E-Value than stated here. In the little combo box below these two values, you can decide to see only hits against the SEED database ('''Just FIG IDs'''), or also against other databases ('''Show all Databases'''). You can '''Sort''' the '''Results By''' ''Score'', ''Percent Identity'' (default) or ''Score per position''. These values locally refer to the hit as known from BLAST hits, so a high percent identity referring to a very small hit region can make this similarity show up as one of the first hits, as shown in the example. Checking '''Group by Genome''' will aggregate all hits to features in the same genome. A blue box will mark hits that belong to the same genome. After selecting the right values, you can press the button '''Resubmit''' to change the evidence view. [[Image:EvidenceFil1.png]] == Tabular Protein Evidence == Activate the second tab of the large page-spanning [[WebComponents/Tabview|TabView]] to see the tabular view of the evidence. You will find most of the information already shown in the visual view, presented differently and enriched with some additional information. Added are the '''Identical Proteins''' and the '''Functionally coupled''' sections, while '''Location''' information is not presented in this tab. === Similarities === The similarity [[WebComponents/Table|table]] lists hits to similar features in the SEED database (or also other databases), like described for the [[SEED_Viewer_Manual/Visual Protein Evidence|Visual Protein Evidence]]. Each row in the table represents a hit. The first column provides a checkbox to select a hit feature. Again, the buttons '''Align Selected''' and '''FASTA Download Selected''' are present and can be used to get to a TCoffee [[SEED_Viewer_Manual/AlignSeqs|alignment page]] or download the protein sequences of the selected features in FASTA format. The two buttons in the column header allow mass selection of the features. '''All''' will select all features visible in the table, '''check to last checked''' lets you select all features up to a selected feature in the [[WebComponents/Table|table]]. The ID of the hit features, as well as a link to the [[SEED_Viewer_Manual/Annotation|annotation page]] is displayed in the column '''Similar FIG Sequence'''. The next four columns describe information to the hit regions of the query and hit features ('''E-value''', '''Percent Identity''', '''Region in Query peg''' and '''Region in Similar Sequence'''). The '''Organism''' of the hit peg and its '''Function''' are shown in the next two columns. If the function is different from the function of the query feature, it is colored. Same function in the table will get the same color. '''Associated Subsystems'' of the feature are displayed in the next column. If the feature is not associated to a subsystem, you will find the text ''None Added'' in the cell. Evidence Code [[Image:EvidenceSims2.png]] [[Image:EvidenceFilter.png]] === Domains === This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the whole length of the protein). The [[WebComponents/Table|table]] lists the '''Domain DB''' (the database for the domain that was hit), the '''ID''' in the domain database, the '''Name''' of the domain, the '''Location''' of the hit in the selected feature, the '''Score''' for the hit against the domain, as well as the '''Function''' of the domain. The table can be exported using the '''export table''' button. Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]]''' in the menu bar. [[Image:EvidenceDomTable.png]] === Identical Proteins === '''Essentially Identical Proteins''' are proteins that share a common sequence, but the start position of the proteins may vary a little. This definition was made because in different databases or close strains of organisms, it often happens that a protein is present, but the start position may be shifted in the finding genes step. So essentially, this table shows aliases of the feature that were based on protein identity. The first column of the [[WebComponents/Table|table]] shows the '''Database''' the alias can be found in, while the second column ('''ID''') offers the alias name and a link to the protein in the respective database. The following two columns describe the '''Organism''' and the '''Assignment''' for the feature for the alias. [[Image:EvidenceEIPs.png]] === Functionally Coupled === This [[WebComponent/Table|table]] lists all [[Glossary#Functional coupling|functionally coupled]] genes in the organism. You can see the '''Score''', the '''ID''' of the feature and the '''Function''' of the feature. [[Image:EvidenceFCs.png]] 279a3e27353a10663fd2dd507533e076f41c9572 2089 2088 2008-11-25T13:46:01Z DanielaBartels 10 /* Similarities */ wikitext text/x-wiki The Evidence Page is divided into two parts via a [[WebComponents/Tabview|TabView]]: The '''Visual Protein Evidence''' and the '''Tabular Protein Evidence'''. == Visual Protein Evidence == After loading the Evidence Page, the first tab of the [[WebComponent/Tabview|TabView]] is selected. It visually shows different pre-computed tool results for the given feature. In this view, you can see evidence for ''Location'' of the product of the gene in the cell, evidence for protein ''Domains'' and evidence that show ''Similarities'' to other features. === Location === '''Location''' stand for location of the product of the feature in the cell. This section presents output for tools that look for transmembrane helices (TM) or signal peptides (SP) in the feature. In the example, you can see five transmembrane helices in the protein identified via the Phobius tool. They are visualized as little boxes, and their location on the line depicts the location of the transmembrane helices in the protein. [[Image:EvidenceLocation.png]] === Domains === This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the whole length of the protein). Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]]''' in the menu bar. [[Image:EvidenceDomain.png]] === Similarities === This section graphically lists evidence for similarities to other features in the SEED database (or also other databases). The '''E-Value Key''' shown on the top defines the colors that are used to display different E-Value ranges for the similarities to the hit features. Hovering over the E-Value Key shows the value range for each color. Each similarity is represented by two bars, showing the alignment of the similarity. The first bar is the '''query''' feature, the second the '''hit''' feature. The abbreviation in front of this bar informs you about the organism the hit feature is in. Hover over the abbreviation to get the complete organism name. Behind the box you can find the [[Glossary#Functional role|functional role]] of the hit feature. The length of the outside box shows the complete length of the respective sequence. The color of the outside box represents the range of the evalue score according to the E-Value Key bar. The length of the inner (white) box depicts the actual section of the sequence the similarity to the other feature is in. Hovering over the box will show you some information about the hit feature (see tooltip graphics below), including the [[Glossary#Functional role|functional role]], the [[Glossary#Subsystem|subsystems]] and some values describing the hit area. If you check some of the checkboxes in front of the [[Glossary#Functional role|functional role]] descriptions of the hit genes, you can access two function via the buttons on top of the Similarity graphics. The button '''Align Selected''' leads to an [[SEED_Viewer_Manual/AlignSeqs|alignment page]] showing a TCoffee alignment for the selected features. '''FASTA Download Selected''' lets you download the selected sequences in aminoacid FASTA format. [[Image:EvidenceSims1.png]] [[Image:EvidenceHoverSim.png]] To change the evidence view with respect to the sorting and the filtering of the hits, you can find a little control box on top of the similarity graphics. '''Max Sims''' is the number of similarities that are listed on the page. '''Max E-Value''' filters out all similarities that have a higher E-Value than stated here. In the little combo box below these two values, you can decide to see only hits against the SEED database ('''Just FIG IDs'''), or also against other databases ('''Show all Databases'''). You can '''Sort''' the '''Results By''' ''Score'', ''Percent Identity'' (default) or ''Score per position''. These values locally refer to the hit as known from BLAST hits, so a high percent identity referring to a very small hit region can make this similarity show up as one of the first hits, as shown in the example. Checking '''Group by Genome''' will aggregate all hits to features in the same genome. A blue box will mark hits that belong to the same genome. After selecting the right values, you can press the button '''Resubmit''' to change the evidence view. [[Image:EvidenceFil1.png]] == Tabular Protein Evidence == Activate the second tab of the large page-spanning [[WebComponents/Tabview|TabView]] to see the tabular view of the evidence. You will find most of the information already shown in the visual view, presented differently and enriched with some additional information. Added are the '''Identical Proteins''' and the '''Functionally coupled''' sections, while '''Location''' information is not presented in this tab. === Similarities === The similarity [[WebComponents/Table|table]] lists hits to similar features in the SEED database (or also other databases), like described for the [[SEED_Viewer_Manual/Visual Protein Evidence|Visual Protein Evidence]]. Each row in the table represents a hit. The first column provides a checkbox to select a hit feature. Again, the buttons '''Align Selected''' and '''FASTA Download Selected''' are present and can be used to get to a TCoffee [[SEED_Viewer_Manual/AlignSeqs|alignment page]] or download the protein sequences of the selected features in FASTA format. The two buttons in the column header allow mass selection of the features. '''All''' will select all features visible in the table, '''check to last checked''' lets you select all features up to a selected feature in the [[WebComponents/Table|table]]. The ID of the hit features, as well as a link to the [[SEED_Viewer_Manual/Annotation|annotation page]] is displayed in the column '''Similar FIG Sequence'''. The next four columns describe information to the hit regions of the query and hit features ('''E-value''', '''Percent Identity''', '''Region in Query peg''' and '''Region in Similar Sequence'''). The '''Organism''' of the hit peg and its '''Function''' are shown in the next two columns. If the function is different from the function of the query feature, it is colored. Same function in the table will get the same color. '''Associated Subsystems'' of the feature are displayed in the next column. If the feature is not associated to a subsystem, you will find the text ''None added'' in the cell. There are three '''Evidence Codes''' that can be found in the last column. ''ISU'' means that the feature is unique in a cell of a subsystem. This means that there is no other feature in the genome that is thought to have the same function. ICW(number) means the feature is clustered with ''number'' features in the genome. ''FF'' says that it is in a [[Glossary#FIGfam|FIGfam]]. The [[WebComponents/Table|table]] can be exported via the button '''export table''' that can be found on top of the table. [[Image:EvidenceSims2.png]] You can filter and sort the table using the [[WebComponents/Tabview|TabView]] above the table. The second tab, '''Sims Filter''' works the same way as described for the [[Image:EvidenceFilter.png]] === Domains === This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the whole length of the protein). The [[WebComponents/Table|table]] lists the '''Domain DB''' (the database for the domain that was hit), the '''ID''' in the domain database, the '''Name''' of the domain, the '''Location''' of the hit in the selected feature, the '''Score''' for the hit against the domain, as well as the '''Function''' of the domain. The table can be exported using the '''export table''' button. Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]]''' in the menu bar. [[Image:EvidenceDomTable.png]] === Identical Proteins === '''Essentially Identical Proteins''' are proteins that share a common sequence, but the start position of the proteins may vary a little. This definition was made because in different databases or close strains of organisms, it often happens that a protein is present, but the start position may be shifted in the finding genes step. So essentially, this table shows aliases of the feature that were based on protein identity. The first column of the [[WebComponents/Table|table]] shows the '''Database''' the alias can be found in, while the second column ('''ID''') offers the alias name and a link to the protein in the respective database. The following two columns describe the '''Organism''' and the '''Assignment''' for the feature for the alias. [[Image:EvidenceEIPs.png]] === Functionally Coupled === This [[WebComponent/Table|table]] lists all [[Glossary#Functional coupling|functionally coupled]] genes in the organism. You can see the '''Score''', the '''ID''' of the feature and the '''Function''' of the feature. [[Image:EvidenceFCs.png]] 2aa9a11c13198bf83d2f035d50ab3490a217dd96 2090 2089 2008-11-25T13:47:29Z DanielaBartels 10 /* Similarities */ wikitext text/x-wiki The Evidence Page is divided into two parts via a [[WebComponents/Tabview|TabView]]: The '''Visual Protein Evidence''' and the '''Tabular Protein Evidence'''. == Visual Protein Evidence == After loading the Evidence Page, the first tab of the [[WebComponent/Tabview|TabView]] is selected. It visually shows different pre-computed tool results for the given feature. In this view, you can see evidence for ''Location'' of the product of the gene in the cell, evidence for protein ''Domains'' and evidence that show ''Similarities'' to other features. === Location === '''Location''' stand for location of the product of the feature in the cell. This section presents output for tools that look for transmembrane helices (TM) or signal peptides (SP) in the feature. In the example, you can see five transmembrane helices in the protein identified via the Phobius tool. They are visualized as little boxes, and their location on the line depicts the location of the transmembrane helices in the protein. [[Image:EvidenceLocation.png]] === Domains === This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the whole length of the protein). Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]]''' in the menu bar. [[Image:EvidenceDomain.png]] === Similarities === This section graphically lists evidence for similarities to other features in the SEED database (or also other databases). The '''E-Value Key''' shown on the top defines the colors that are used to display different E-Value ranges for the similarities to the hit features. Hovering over the E-Value Key shows the value range for each color. Each similarity is represented by two bars, showing the alignment of the similarity. The first bar is the '''query''' feature, the second the '''hit''' feature. The abbreviation in front of this bar informs you about the organism the hit feature is in. Hover over the abbreviation to get the complete organism name. Behind the box you can find the [[Glossary#Functional role|functional role]] of the hit feature. The length of the outside box shows the complete length of the respective sequence. The color of the outside box represents the range of the evalue score according to the E-Value Key bar. The length of the inner (white) box depicts the actual section of the sequence the similarity to the other feature is in. Hovering over the box will show you some information about the hit feature (see tooltip graphics below), including the [[Glossary#Functional role|functional role]], the [[Glossary#Subsystem|subsystems]] and some values describing the hit area. If you check some of the checkboxes in front of the [[Glossary#Functional role|functional role]] descriptions of the hit genes, you can access two function via the buttons on top of the Similarity graphics. The button '''Align Selected''' leads to an [[SEED_Viewer_Manual/AlignSeqs|alignment page]] showing a TCoffee alignment for the selected features. '''FASTA Download Selected''' lets you download the selected sequences in aminoacid FASTA format. [[Image:EvidenceSims1.png]] [[Image:EvidenceHoverSim.png]] To change the evidence view with respect to the sorting and the filtering of the hits, you can find a little control box on top of the similarity graphics. '''Max Sims''' is the number of similarities that are listed on the page. '''Max E-Value''' filters out all similarities that have a higher E-Value than stated here. In the little combo box below these two values, you can decide to see only hits against the SEED database ('''Just FIG IDs'''), or also against other databases ('''Show all Databases'''). You can '''Sort''' the '''Results By''' ''Score'', ''Percent Identity'' (default) or ''Score per position''. These values locally refer to the hit as known from BLAST hits, so a high percent identity referring to a very small hit region can make this similarity show up as one of the first hits, as shown in the example. Checking '''Group by Genome''' will aggregate all hits to features in the same genome. A blue box will mark hits that belong to the same genome. After selecting the right values, you can press the button '''Resubmit''' to change the evidence view. [[Image:EvidenceFil1.png]] == Tabular Protein Evidence == Activate the second tab of the large page-spanning [[WebComponents/Tabview|TabView]] to see the tabular view of the evidence. You will find most of the information already shown in the visual view, presented differently and enriched with some additional information. Added are the '''Identical Proteins''' and the '''Functionally coupled''' sections, while '''Location''' information is not presented in this tab. === Similarities === The similarity [[WebComponents/Table|table]] lists hits to similar features in the SEED database (or also other databases), like described for the [[SEED_Viewer_Manual/Visual Protein Evidence|Visual Protein Evidence]]. Each row in the table represents a hit. The first column provides a checkbox to select a hit feature. Again, the buttons '''Align Selected''' and '''FASTA Download Selected''' are present and can be used to get to a TCoffee [[SEED_Viewer_Manual/AlignSeqs|alignment page]] or download the protein sequences of the selected features in FASTA format. The two buttons in the column header allow mass selection of the features. '''All''' will select all features visible in the table, '''check to last checked''' lets you select all features up to a selected feature in the [[WebComponents/Table|table]]. The ID of the hit features, as well as a link to the [[SEED_Viewer_Manual/Annotation|annotation page]] is displayed in the column '''Similar FIG Sequence'''. The next four columns describe information to the hit regions of the query and hit features ('''E-value''', '''Percent Identity''', '''Region in Query peg''' and '''Region in Similar Sequence'''). The '''Organism''' of the hit peg and its '''Function''' are shown in the next two columns. If the function is different from the function of the query feature, it is colored. Same function in the table will get the same color. '''Associated Subsystems'' of the feature are displayed in the next column. If the feature is not associated to a subsystem, you will find the text ''None added'' in the cell. There are three '''Evidence Codes''' that can be found in the last column. ''ISU'' means that the feature is unique in a cell of a subsystem. This means that there is no other feature in the genome that is thought to have the same function. ICW(number) means the feature is clustered with ''number'' features in the genome. ''FF'' says that it is in a [[Glossary#FIGfam|FIGfam]]. The [[WebComponents/Table|table]] can be exported via the button '''export table''' that can be found on top of the table. [[Image:EvidenceSims2.png]] You can filter and sort the table using the [[WebComponents/Tabview|TabView]] above the table. The second tab, '''Sims Filter''' works the same way as described for the Similarities in the [[SEED_Viewer_Manual/Visual Protein Evidence|Visual Protein Evidence]]. [[Image:EvidenceFilter.png]] === Domains === This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the whole length of the protein). The [[WebComponents/Table|table]] lists the '''Domain DB''' (the database for the domain that was hit), the '''ID''' in the domain database, the '''Name''' of the domain, the '''Location''' of the hit in the selected feature, the '''Score''' for the hit against the domain, as well as the '''Function''' of the domain. The table can be exported using the '''export table''' button. Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]]''' in the menu bar. [[Image:EvidenceDomTable.png]] === Identical Proteins === '''Essentially Identical Proteins''' are proteins that share a common sequence, but the start position of the proteins may vary a little. This definition was made because in different databases or close strains of organisms, it often happens that a protein is present, but the start position may be shifted in the finding genes step. So essentially, this table shows aliases of the feature that were based on protein identity. The first column of the [[WebComponents/Table|table]] shows the '''Database''' the alias can be found in, while the second column ('''ID''') offers the alias name and a link to the protein in the respective database. The following two columns describe the '''Organism''' and the '''Assignment''' for the feature for the alias. [[Image:EvidenceEIPs.png]] === Functionally Coupled === This [[WebComponent/Table|table]] lists all [[Glossary#Functional coupling|functionally coupled]] genes in the organism. You can see the '''Score''', the '''ID''' of the feature and the '''Function''' of the feature. [[Image:EvidenceFCs.png]] 4e324e0c81d161e5812490aa508a0a755d418dae 2091 2090 2008-11-25T13:52:25Z DanielaBartels 10 /* Similarities */ wikitext text/x-wiki The Evidence Page is divided into two parts via a [[WebComponents/Tabview|TabView]]: The '''Visual Protein Evidence''' and the '''Tabular Protein Evidence'''. == Visual Protein Evidence == After loading the Evidence Page, the first tab of the [[WebComponent/Tabview|TabView]] is selected. It visually shows different pre-computed tool results for the given feature. In this view, you can see evidence for ''Location'' of the product of the gene in the cell, evidence for protein ''Domains'' and evidence that show ''Similarities'' to other features. === Location === '''Location''' stand for location of the product of the feature in the cell. This section presents output for tools that look for transmembrane helices (TM) or signal peptides (SP) in the feature. In the example, you can see five transmembrane helices in the protein identified via the Phobius tool. They are visualized as little boxes, and their location on the line depicts the location of the transmembrane helices in the protein. [[Image:EvidenceLocation.png]] === Domains === This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the whole length of the protein). Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]]''' in the menu bar. [[Image:EvidenceDomain.png]] === Similarities === This section graphically lists evidence for similarities to other features in the SEED database (or also other databases). The '''E-Value Key''' shown on the top defines the colors that are used to display different E-Value ranges for the similarities to the hit features. Hovering over the E-Value Key shows the value range for each color. Each similarity is represented by two bars, showing the alignment of the similarity. The first bar is the '''query''' feature, the second the '''hit''' feature. The abbreviation in front of this bar informs you about the organism the hit feature is in. Hover over the abbreviation to get the complete organism name. Behind the box you can find the [[Glossary#Functional role|functional role]] of the hit feature. The length of the outside box shows the complete length of the respective sequence. The color of the outside box represents the range of the evalue score according to the E-Value Key bar. The length of the inner (white) box depicts the actual section of the sequence the similarity to the other feature is in. Hovering over the box will show you some information about the hit feature (see tooltip graphics below), including the [[Glossary#Functional role|functional role]], the [[Glossary#Subsystem|subsystems]] and some values describing the hit area. If you check some of the checkboxes in front of the [[Glossary#Functional role|functional role]] descriptions of the hit genes, you can access two function via the buttons on top of the Similarity graphics. The button '''Align Selected''' leads to an [[SEED_Viewer_Manual/AlignSeqs|alignment page]] showing a TCoffee alignment for the selected features. '''FASTA Download Selected''' lets you download the selected sequences in aminoacid FASTA format. [[Image:EvidenceSims1.png]] [[Image:EvidenceHoverSim.png]] To change the evidence view with respect to the sorting and the filtering of the hits, you can find a little control box on top of the similarity graphics. '''Max Sims''' is the number of similarities that are listed on the page. '''Max E-Value''' filters out all similarities that have a higher E-Value than stated here. In the little combo box below these two values, you can decide to see only hits against the SEED database ('''Just FIG IDs'''), or also against other databases ('''Show all Databases'''). You can '''Sort''' the '''Results By''' ''Score'', ''Percent Identity'' (default) or ''Score per position''. These values locally refer to the hit as known from BLAST hits, so a high percent identity referring to a very small hit region can make this similarity show up as one of the first hits, as shown in the example. Checking '''Group by Genome''' will aggregate all hits to features in the same genome. A blue box will mark hits that belong to the same genome. After selecting the right values, you can press the button '''Resubmit''' to change the evidence view. [[Image:EvidenceFil1.png]] == Tabular Protein Evidence == Activate the second tab of the large page-spanning [[WebComponents/Tabview|TabView]] to see the tabular view of the evidence. You will find most of the information already shown in the visual view, presented differently and enriched with some additional information. Added are the '''Identical Proteins''' and the '''Functionally coupled''' sections, while '''Location''' information is not presented in this tab. === Similarities === The similarity [[WebComponents/Table|table]] lists hits to similar features in the SEED database (or also other databases), like described for the [[SEED_Viewer_Manual/Visual Protein Evidence|Visual Protein Evidence]]. Each row in the table represents a hit. The first column provides a checkbox to select a hit feature. Again, the buttons '''Align Selected''' and '''FASTA Download Selected''' are present and can be used to get to a TCoffee [[SEED_Viewer_Manual/AlignSeqs|alignment page]] or download the protein sequences of the selected features in FASTA format. The two buttons in the column header allow mass selection of the features. '''All''' will select all features visible in the table, '''check to last checked''' lets you select all features up to a selected feature in the [[WebComponents/Table|table]]. The ID of the hit features, as well as a link to the [[SEED_Viewer_Manual/Annotation|annotation page]] is displayed in the column '''Similar FIG Sequence'''. The next four columns describe information to the hit regions of the query and hit features ('''E-value''', '''Percent Identity''', '''Region in Query peg''' and '''Region in Similar Sequence'''). The '''Organism''' of the hit peg and its '''Function''' are shown in the next two columns. If the function is different from the function of the query feature, it is colored. Same function in the table will get the same color. '''Associated Subsystems'' of the feature are displayed in the next column. If the feature is not associated to a subsystem, you will find the text ''None added'' in the cell. There are three '''Evidence Codes''' that can be found in the last column. ''ISU'' means that the feature is unique in a cell of a subsystem. This means that there is no other feature in the genome that is thought to have the same function. ICW(number) means the feature is clustered with ''number'' features in the genome. ''FF'' says that it is in a [[Glossary#FIGfam|FIGfam]]. The [[WebComponents/Table|table]] can be exported via the button '''export table''' that can be found on top of the table. [[Image:EvidenceSims2.png]] You can filter and sort the table using the [[WebComponents/Tabview|TabView]] above the table. The second tab, '''Sims Filter''' works the same way as described for the Similarities in the [[SEED_Viewer_Manual/Evidence#Visual Protein Evidence|Visual Protein Evidence]]. The first tab '''Edit Columns''' contains a number of columns with additional information that can be added to the display of the table ([[Glossary#FIGfams|FIGfams]], different aliases to other databases and many others). [[Image:EvidenceFilter.png]] === Domains === This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the whole length of the protein). The [[WebComponents/Table|table]] lists the '''Domain DB''' (the database for the domain that was hit), the '''ID''' in the domain database, the '''Name''' of the domain, the '''Location''' of the hit in the selected feature, the '''Score''' for the hit against the domain, as well as the '''Function''' of the domain. The table can be exported using the '''export table''' button. Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]]''' in the menu bar. [[Image:EvidenceDomTable.png]] === Identical Proteins === '''Essentially Identical Proteins''' are proteins that share a common sequence, but the start position of the proteins may vary a little. This definition was made because in different databases or close strains of organisms, it often happens that a protein is present, but the start position may be shifted in the finding genes step. So essentially, this table shows aliases of the feature that were based on protein identity. The first column of the [[WebComponents/Table|table]] shows the '''Database''' the alias can be found in, while the second column ('''ID''') offers the alias name and a link to the protein in the respective database. The following two columns describe the '''Organism''' and the '''Assignment''' for the feature for the alias. [[Image:EvidenceEIPs.png]] === Functionally Coupled === This [[WebComponent/Table|table]] lists all [[Glossary#Functional coupling|functionally coupled]] genes in the organism. You can see the '''Score''', the '''ID''' of the feature and the '''Function''' of the feature. [[Image:EvidenceFCs.png]] 8220742a5b211b9dfac278d816af179cb3d5b361 2092 2091 2008-11-25T13:53:43Z DanielaBartels 10 /* Similarities */ wikitext text/x-wiki The Evidence Page is divided into two parts via a [[WebComponents/Tabview|TabView]]: The '''Visual Protein Evidence''' and the '''Tabular Protein Evidence'''. == Visual Protein Evidence == After loading the Evidence Page, the first tab of the [[WebComponent/Tabview|TabView]] is selected. It visually shows different pre-computed tool results for the given feature. In this view, you can see evidence for ''Location'' of the product of the gene in the cell, evidence for protein ''Domains'' and evidence that show ''Similarities'' to other features. === Location === '''Location''' stand for location of the product of the feature in the cell. This section presents output for tools that look for transmembrane helices (TM) or signal peptides (SP) in the feature. In the example, you can see five transmembrane helices in the protein identified via the Phobius tool. They are visualized as little boxes, and their location on the line depicts the location of the transmembrane helices in the protein. [[Image:EvidenceLocation.png]] === Domains === This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the whole length of the protein). Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]]''' in the menu bar. [[Image:EvidenceDomain.png]] === Similarities === This section graphically lists evidence for similarities to other features in the SEED database (or also other databases). The '''E-Value Key''' shown on the top defines the colors that are used to display different E-Value ranges for the similarities to the hit features. Hovering over the E-Value Key shows the value range for each color. Each similarity is represented by two bars, showing the alignment of the similarity. The first bar is the '''query''' feature, the second the '''hit''' feature. The abbreviation in front of this bar informs you about the organism the hit feature is in. Hover over the abbreviation to get the complete organism name. Behind the box you can find the [[Glossary#Functional role|functional role]] of the hit feature. The length of the outside box shows the complete length of the respective sequence. The color of the outside box represents the range of the evalue score according to the E-Value Key bar. The length of the inner (white) box depicts the actual section of the sequence the similarity to the other feature is in. Hovering over the box will show you some information about the hit feature (see tooltip graphics below), including the [[Glossary#Functional role|functional role]], the [[Glossary#Subsystem|subsystems]] and some values describing the hit area. If you check some of the checkboxes in front of the [[Glossary#Functional role|functional role]] descriptions of the hit genes, you can access two function via the buttons on top of the Similarity graphics. The button '''Align Selected''' leads to an [[SEED_Viewer_Manual/AlignSeqs|alignment page]] showing a TCoffee alignment for the selected features. '''FASTA Download Selected''' lets you download the selected sequences in aminoacid FASTA format. [[Image:EvidenceSims1.png]] [[Image:EvidenceHoverSim.png]] To change the evidence view with respect to the sorting and the filtering of the hits, you can find a little control box on top of the similarity graphics. '''Max Sims''' is the number of similarities that are listed on the page. '''Max E-Value''' filters out all similarities that have a higher E-Value than stated here. In the little combo box below these two values, you can decide to see only hits against the SEED database ('''Just FIG IDs'''), or also against other databases ('''Show all Databases'''). You can '''Sort''' the '''Results By''' ''Score'', ''Percent Identity'' (default) or ''Score per position''. These values locally refer to the hit as known from BLAST hits, so a high percent identity referring to a very small hit region can make this similarity show up as one of the first hits, as shown in the example. Checking '''Group by Genome''' will aggregate all hits to features in the same genome. A blue box will mark hits that belong to the same genome. After selecting the right values, you can press the button '''Resubmit''' to change the evidence view. [[Image:EvidenceFil1.png]] == Tabular Protein Evidence == Activate the second tab of the large page-spanning [[WebComponents/Tabview|TabView]] to see the tabular view of the evidence. You will find most of the information already shown in the visual view, presented differently and enriched with some additional information. Added are the '''Identical Proteins''' and the '''Functionally coupled''' sections, while '''Location''' information is not presented in this tab. === Similarities === The similarity [[WebComponents/Table|table]] lists hits to similar features in the SEED database (or also other databases), like described for the [[SEED_Viewer_Manual/Visual Protein Evidence|Visual Protein Evidence]]. Each row in the table represents a hit. The first column provides a checkbox to select a hit feature. Again, the buttons '''Align Selected''' and '''FASTA Download Selected''' are present and can be used to get to a TCoffee [[SEED_Viewer_Manual/AlignSeqs|alignment page]] or download the protein sequences of the selected features in FASTA format. The two buttons in the column header allow mass selection of the features. '''All''' will select all features visible in the table, '''check to last checked''' lets you select all features up to a selected feature in the [[WebComponents/Table|table]]. The ID of the hit features, as well as a link to the [[SEED_Viewer_Manual/Annotation|annotation page]] is displayed in the column '''Similar FIG Sequence'''. The next four columns describe information to the hit regions of the query and hit features ('''E-value''', '''Percent Identity''', '''Region in Query peg''' and '''Region in Similar Sequence'''). The '''Organism''' of the hit peg and its '''Function''' are shown in the next two columns. If the function is different from the function of the query feature, it is colored. Same function in the table will get the same color. '''Associated Subsystems'' of the feature are displayed in the next column. If the feature is not associated to a subsystem, you will find the text ''None added'' in the cell. There are three '''Evidence Codes''' that can be found in the last column. ''ISU'' means that the feature is unique in a cell of a subsystem. This means that there is no other feature in the genome that is thought to have the same function. ICW(number) means the feature is clustered with ''number'' features in the genome. ''FF'' says that it is in a [[Glossary#FIGfam|FIGfam]]. The [[WebComponents/Table|table]] can be exported via the button '''export table''' that can be found on top of the table. [[Image:EvidenceSims2.png]] You can filter and sort the table using the [[WebComponents/Tabview|TabView]] above the table. The second tab, '''Sims Filter''' works the same way as described for the Similarities in the [[SEED_Viewer_Manual/Evidence#Visual Protein Evidence|Visual Protein Evidence]]. The first tab '''Edit Columns''' contains a number of columns with additional information that can be added to the display of the table ([[Glossary#FIGfams|FIGfams]], different aliases to other databases and many others). Just choose a column name, press the arrow to put it into the right field and it will add it to the table. [[Image:EvidenceFilter.png]] === Domains === This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the whole length of the protein). The [[WebComponents/Table|table]] lists the '''Domain DB''' (the database for the domain that was hit), the '''ID''' in the domain database, the '''Name''' of the domain, the '''Location''' of the hit in the selected feature, the '''Score''' for the hit against the domain, as well as the '''Function''' of the domain. The table can be exported using the '''export table''' button. Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]]''' in the menu bar. [[Image:EvidenceDomTable.png]] === Identical Proteins === '''Essentially Identical Proteins''' are proteins that share a common sequence, but the start position of the proteins may vary a little. This definition was made because in different databases or close strains of organisms, it often happens that a protein is present, but the start position may be shifted in the finding genes step. So essentially, this table shows aliases of the feature that were based on protein identity. The first column of the [[WebComponents/Table|table]] shows the '''Database''' the alias can be found in, while the second column ('''ID''') offers the alias name and a link to the protein in the respective database. The following two columns describe the '''Organism''' and the '''Assignment''' for the feature for the alias. [[Image:EvidenceEIPs.png]] === Functionally Coupled === This [[WebComponent/Table|table]] lists all [[Glossary#Functional coupling|functionally coupled]] genes in the organism. You can see the '''Score''', the '''ID''' of the feature and the '''Function''' of the feature. [[Image:EvidenceFCs.png]] a7724104a1d64f0ef0e02640c6d816e1100c73a3 2093 2092 2008-11-25T13:55:19Z DanielaBartels 10 wikitext text/x-wiki The Evidence Page is divided into two parts via a [[WebComponents/Tabview|TabView]]: The '''Visual Protein Evidence''' and the '''Tabular Protein Evidence'''. If you are logged in and the feature belongs to your private genome, this page will have additional options for you to annotate the feature. These are described [[SEED_Viewer_Manual/Editing_Capabilities/Evidence|here]]. == Visual Protein Evidence == After loading the Evidence Page, the first tab of the [[WebComponent/Tabview|TabView]] is selected. It visually shows different pre-computed tool results for the given feature. In this view, you can see evidence for ''Location'' of the product of the gene in the cell, evidence for protein ''Domains'' and evidence that show ''Similarities'' to other features. === Location === '''Location''' stand for location of the product of the feature in the cell. This section presents output for tools that look for transmembrane helices (TM) or signal peptides (SP) in the feature. In the example, you can see five transmembrane helices in the protein identified via the Phobius tool. They are visualized as little boxes, and their location on the line depicts the location of the transmembrane helices in the protein. [[Image:EvidenceLocation.png]] === Domains === This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the whole length of the protein). Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]]''' in the menu bar. [[Image:EvidenceDomain.png]] === Similarities === This section graphically lists evidence for similarities to other features in the SEED database (or also other databases). The '''E-Value Key''' shown on the top defines the colors that are used to display different E-Value ranges for the similarities to the hit features. Hovering over the E-Value Key shows the value range for each color. Each similarity is represented by two bars, showing the alignment of the similarity. The first bar is the '''query''' feature, the second the '''hit''' feature. The abbreviation in front of this bar informs you about the organism the hit feature is in. Hover over the abbreviation to get the complete organism name. Behind the box you can find the [[Glossary#Functional role|functional role]] of the hit feature. The length of the outside box shows the complete length of the respective sequence. The color of the outside box represents the range of the evalue score according to the E-Value Key bar. The length of the inner (white) box depicts the actual section of the sequence the similarity to the other feature is in. Hovering over the box will show you some information about the hit feature (see tooltip graphics below), including the [[Glossary#Functional role|functional role]], the [[Glossary#Subsystem|subsystems]] and some values describing the hit area. If you check some of the checkboxes in front of the [[Glossary#Functional role|functional role]] descriptions of the hit genes, you can access two function via the buttons on top of the Similarity graphics. The button '''Align Selected''' leads to an [[SEED_Viewer_Manual/AlignSeqs|alignment page]] showing a TCoffee alignment for the selected features. '''FASTA Download Selected''' lets you download the selected sequences in aminoacid FASTA format. [[Image:EvidenceSims1.png]] [[Image:EvidenceHoverSim.png]] To change the evidence view with respect to the sorting and the filtering of the hits, you can find a little control box on top of the similarity graphics. '''Max Sims''' is the number of similarities that are listed on the page. '''Max E-Value''' filters out all similarities that have a higher E-Value than stated here. In the little combo box below these two values, you can decide to see only hits against the SEED database ('''Just FIG IDs'''), or also against other databases ('''Show all Databases'''). You can '''Sort''' the '''Results By''' ''Score'', ''Percent Identity'' (default) or ''Score per position''. These values locally refer to the hit as known from BLAST hits, so a high percent identity referring to a very small hit region can make this similarity show up as one of the first hits, as shown in the example. Checking '''Group by Genome''' will aggregate all hits to features in the same genome. A blue box will mark hits that belong to the same genome. After selecting the right values, you can press the button '''Resubmit''' to change the evidence view. [[Image:EvidenceFil1.png]] == Tabular Protein Evidence == Activate the second tab of the large page-spanning [[WebComponents/Tabview|TabView]] to see the tabular view of the evidence. You will find most of the information already shown in the visual view, presented differently and enriched with some additional information. Added are the '''Identical Proteins''' and the '''Functionally coupled''' sections, while '''Location''' information is not presented in this tab. === Similarities === The similarity [[WebComponents/Table|table]] lists hits to similar features in the SEED database (or also other databases), like described for the [[SEED_Viewer_Manual/Visual Protein Evidence|Visual Protein Evidence]]. Each row in the table represents a hit. The first column provides a checkbox to select a hit feature. Again, the buttons '''Align Selected''' and '''FASTA Download Selected''' are present and can be used to get to a TCoffee [[SEED_Viewer_Manual/AlignSeqs|alignment page]] or download the protein sequences of the selected features in FASTA format. The two buttons in the column header allow mass selection of the features. '''All''' will select all features visible in the table, '''check to last checked''' lets you select all features up to a selected feature in the [[WebComponents/Table|table]]. The ID of the hit features, as well as a link to the [[SEED_Viewer_Manual/Annotation|annotation page]] is displayed in the column '''Similar FIG Sequence'''. The next four columns describe information to the hit regions of the query and hit features ('''E-value''', '''Percent Identity''', '''Region in Query peg''' and '''Region in Similar Sequence'''). The '''Organism''' of the hit peg and its '''Function''' are shown in the next two columns. If the function is different from the function of the query feature, it is colored. Same function in the table will get the same color. '''Associated Subsystems'' of the feature are displayed in the next column. If the feature is not associated to a subsystem, you will find the text ''None added'' in the cell. There are three '''Evidence Codes''' that can be found in the last column. ''ISU'' means that the feature is unique in a cell of a subsystem. This means that there is no other feature in the genome that is thought to have the same function. ICW(number) means the feature is clustered with ''number'' features in the genome. ''FF'' says that it is in a [[Glossary#FIGfam|FIGfam]]. The [[WebComponents/Table|table]] can be exported via the button '''export table''' that can be found on top of the table. [[Image:EvidenceSims2.png]] You can filter and sort the table using the [[WebComponents/Tabview|TabView]] above the table. The second tab, '''Sims Filter''' works the same way as described for the Similarities in the [[SEED_Viewer_Manual/Evidence#Visual Protein Evidence|Visual Protein Evidence]]. The first tab '''Edit Columns''' contains a number of columns with additional information that can be added to the display of the table ([[Glossary#FIGfams|FIGfams]], different aliases to other databases and many others). Just choose a column name, press the arrow to put it into the right field and it will add it to the table. [[Image:EvidenceFilter.png]] === Domains === This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the whole length of the protein). The [[WebComponents/Table|table]] lists the '''Domain DB''' (the database for the domain that was hit), the '''ID''' in the domain database, the '''Name''' of the domain, the '''Location''' of the hit in the selected feature, the '''Score''' for the hit against the domain, as well as the '''Function''' of the domain. The table can be exported using the '''export table''' button. Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]]''' in the menu bar. [[Image:EvidenceDomTable.png]] === Identical Proteins === '''Essentially Identical Proteins''' are proteins that share a common sequence, but the start position of the proteins may vary a little. This definition was made because in different databases or close strains of organisms, it often happens that a protein is present, but the start position may be shifted in the finding genes step. So essentially, this table shows aliases of the feature that were based on protein identity. The first column of the [[WebComponents/Table|table]] shows the '''Database''' the alias can be found in, while the second column ('''ID''') offers the alias name and a link to the protein in the respective database. The following two columns describe the '''Organism''' and the '''Assignment''' for the feature for the alias. [[Image:EvidenceEIPs.png]] === Functionally Coupled === This [[WebComponent/Table|table]] lists all [[Glossary#Functional coupling|functionally coupled]] genes in the organism. You can see the '''Score''', the '''ID''' of the feature and the '''Function''' of the feature. [[Image:EvidenceFCs.png]] 63cb31e320f955a327a36b63feb0fb60d3494e61 2094 2093 2008-11-25T13:56:40Z TobiasPaczian 17 /* Domains */ wikitext text/x-wiki The Evidence Page is divided into two parts via a [[WebComponents/Tabview|TabView]]: The '''Visual Protein Evidence''' and the '''Tabular Protein Evidence'''. If you are logged in and the feature belongs to your private genome, this page will have additional options for you to annotate the feature. These are described [[SEED_Viewer_Manual/Editing_Capabilities/Evidence|here]]. == Visual Protein Evidence == After loading the Evidence Page, the first tab of the [[WebComponent/Tabview|TabView]] is selected. It visually shows different pre-computed tool results for the given feature. In this view, you can see evidence for ''Location'' of the product of the gene in the cell, evidence for protein ''Domains'' and evidence that show ''Similarities'' to other features. === Location === '''Location''' stand for location of the product of the feature in the cell. This section presents output for tools that look for transmembrane helices (TM) or signal peptides (SP) in the feature. In the example, you can see five transmembrane helices in the protein identified via the Phobius tool. They are visualized as little boxes, and their location on the line depicts the location of the transmembrane helices in the protein. [[Image:EvidenceLocation.png]] === Domains === This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the full length of the protein). Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]]''' in the menu bar. [[Image:EvidenceDomain.png]] === Similarities === This section graphically lists evidence for similarities to other features in the SEED database (or also other databases). The '''E-Value Key''' shown on the top defines the colors that are used to display different E-Value ranges for the similarities to the hit features. Hovering over the E-Value Key shows the value range for each color. Each similarity is represented by two bars, showing the alignment of the similarity. The first bar is the '''query''' feature, the second the '''hit''' feature. The abbreviation in front of this bar informs you about the organism the hit feature is in. Hover over the abbreviation to get the complete organism name. Behind the box you can find the [[Glossary#Functional role|functional role]] of the hit feature. The length of the outside box shows the complete length of the respective sequence. The color of the outside box represents the range of the evalue score according to the E-Value Key bar. The length of the inner (white) box depicts the actual section of the sequence the similarity to the other feature is in. Hovering over the box will show you some information about the hit feature (see tooltip graphics below), including the [[Glossary#Functional role|functional role]], the [[Glossary#Subsystem|subsystems]] and some values describing the hit area. If you check some of the checkboxes in front of the [[Glossary#Functional role|functional role]] descriptions of the hit genes, you can access two function via the buttons on top of the Similarity graphics. The button '''Align Selected''' leads to an [[SEED_Viewer_Manual/AlignSeqs|alignment page]] showing a TCoffee alignment for the selected features. '''FASTA Download Selected''' lets you download the selected sequences in aminoacid FASTA format. [[Image:EvidenceSims1.png]] [[Image:EvidenceHoverSim.png]] To change the evidence view with respect to the sorting and the filtering of the hits, you can find a little control box on top of the similarity graphics. '''Max Sims''' is the number of similarities that are listed on the page. '''Max E-Value''' filters out all similarities that have a higher E-Value than stated here. In the little combo box below these two values, you can decide to see only hits against the SEED database ('''Just FIG IDs'''), or also against other databases ('''Show all Databases'''). You can '''Sort''' the '''Results By''' ''Score'', ''Percent Identity'' (default) or ''Score per position''. These values locally refer to the hit as known from BLAST hits, so a high percent identity referring to a very small hit region can make this similarity show up as one of the first hits, as shown in the example. Checking '''Group by Genome''' will aggregate all hits to features in the same genome. A blue box will mark hits that belong to the same genome. After selecting the right values, you can press the button '''Resubmit''' to change the evidence view. [[Image:EvidenceFil1.png]] == Tabular Protein Evidence == Activate the second tab of the large page-spanning [[WebComponents/Tabview|TabView]] to see the tabular view of the evidence. You will find most of the information already shown in the visual view, presented differently and enriched with some additional information. Added are the '''Identical Proteins''' and the '''Functionally coupled''' sections, while '''Location''' information is not presented in this tab. === Similarities === The similarity [[WebComponents/Table|table]] lists hits to similar features in the SEED database (or also other databases), like described for the [[SEED_Viewer_Manual/Visual Protein Evidence|Visual Protein Evidence]]. Each row in the table represents a hit. The first column provides a checkbox to select a hit feature. Again, the buttons '''Align Selected''' and '''FASTA Download Selected''' are present and can be used to get to a TCoffee [[SEED_Viewer_Manual/AlignSeqs|alignment page]] or download the protein sequences of the selected features in FASTA format. The two buttons in the column header allow mass selection of the features. '''All''' will select all features visible in the table, '''check to last checked''' lets you select all features up to a selected feature in the [[WebComponents/Table|table]]. The ID of the hit features, as well as a link to the [[SEED_Viewer_Manual/Annotation|annotation page]] is displayed in the column '''Similar FIG Sequence'''. The next four columns describe information to the hit regions of the query and hit features ('''E-value''', '''Percent Identity''', '''Region in Query peg''' and '''Region in Similar Sequence'''). The '''Organism''' of the hit peg and its '''Function''' are shown in the next two columns. If the function is different from the function of the query feature, it is colored. Same function in the table will get the same color. '''Associated Subsystems'' of the feature are displayed in the next column. If the feature is not associated to a subsystem, you will find the text ''None added'' in the cell. There are three '''Evidence Codes''' that can be found in the last column. ''ISU'' means that the feature is unique in a cell of a subsystem. This means that there is no other feature in the genome that is thought to have the same function. ICW(number) means the feature is clustered with ''number'' features in the genome. ''FF'' says that it is in a [[Glossary#FIGfam|FIGfam]]. The [[WebComponents/Table|table]] can be exported via the button '''export table''' that can be found on top of the table. [[Image:EvidenceSims2.png]] You can filter and sort the table using the [[WebComponents/Tabview|TabView]] above the table. The second tab, '''Sims Filter''' works the same way as described for the Similarities in the [[SEED_Viewer_Manual/Evidence#Visual Protein Evidence|Visual Protein Evidence]]. The first tab '''Edit Columns''' contains a number of columns with additional information that can be added to the display of the table ([[Glossary#FIGfams|FIGfams]], different aliases to other databases and many others). Just choose a column name, press the arrow to put it into the right field and it will add it to the table. [[Image:EvidenceFilter.png]] === Domains === This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the whole length of the protein). The [[WebComponents/Table|table]] lists the '''Domain DB''' (the database for the domain that was hit), the '''ID''' in the domain database, the '''Name''' of the domain, the '''Location''' of the hit in the selected feature, the '''Score''' for the hit against the domain, as well as the '''Function''' of the domain. The table can be exported using the '''export table''' button. Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]]''' in the menu bar. [[Image:EvidenceDomTable.png]] === Identical Proteins === '''Essentially Identical Proteins''' are proteins that share a common sequence, but the start position of the proteins may vary a little. This definition was made because in different databases or close strains of organisms, it often happens that a protein is present, but the start position may be shifted in the finding genes step. So essentially, this table shows aliases of the feature that were based on protein identity. The first column of the [[WebComponents/Table|table]] shows the '''Database''' the alias can be found in, while the second column ('''ID''') offers the alias name and a link to the protein in the respective database. The following two columns describe the '''Organism''' and the '''Assignment''' for the feature for the alias. [[Image:EvidenceEIPs.png]] === Functionally Coupled === This [[WebComponent/Table|table]] lists all [[Glossary#Functional coupling|functionally coupled]] genes in the organism. You can see the '''Score''', the '''ID''' of the feature and the '''Function''' of the feature. [[Image:EvidenceFCs.png]] cc918b5898d6ec2b81d6dbf33a385951af20e8e7 2096 2094 2008-11-25T13:57:21Z TobiasPaczian 17 /* Similarities */ wikitext text/x-wiki The Evidence Page is divided into two parts via a [[WebComponents/Tabview|TabView]]: The '''Visual Protein Evidence''' and the '''Tabular Protein Evidence'''. If you are logged in and the feature belongs to your private genome, this page will have additional options for you to annotate the feature. These are described [[SEED_Viewer_Manual/Editing_Capabilities/Evidence|here]]. == Visual Protein Evidence == After loading the Evidence Page, the first tab of the [[WebComponent/Tabview|TabView]] is selected. It visually shows different pre-computed tool results for the given feature. In this view, you can see evidence for ''Location'' of the product of the gene in the cell, evidence for protein ''Domains'' and evidence that show ''Similarities'' to other features. === Location === '''Location''' stand for location of the product of the feature in the cell. This section presents output for tools that look for transmembrane helices (TM) or signal peptides (SP) in the feature. In the example, you can see five transmembrane helices in the protein identified via the Phobius tool. They are visualized as little boxes, and their location on the line depicts the location of the transmembrane helices in the protein. [[Image:EvidenceLocation.png]] === Domains === This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the full length of the protein). Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]]''' in the menu bar. [[Image:EvidenceDomain.png]] === Similarities === This section graphically lists evidence for similarities to other features in the SEED and other databases. The '''E-Value Key''' shown on the top defines the colors that are used to display different E-Value ranges for the similarities to the hit features. Hovering over the E-Value Key shows the value range for each color. Each similarity is represented by two bars, showing the alignment of the similarity. The first bar is the '''query''' feature, the second the '''hit''' feature. The abbreviation in front of this bar informs you about the organism the hit feature is in. Hover over the abbreviation to get the complete organism name. Behind the box you can find the [[Glossary#Functional role|functional role]] of the hit feature. The length of the outside box shows the complete length of the respective sequence. The color of the outside box represents the range of the evalue score according to the E-Value Key bar. The length of the inner (white) box depicts the actual section of the sequence the similarity to the other feature is in. Hovering over the box will show you some information about the hit feature (see tooltip graphics below), including the [[Glossary#Functional role|functional role]], the [[Glossary#Subsystem|subsystems]] and some values describing the hit area. If you check some of the checkboxes in front of the [[Glossary#Functional role|functional role]] descriptions of the hit genes, you can access two function via the buttons on top of the Similarity graphics. The button '''Align Selected''' leads to an [[SEED_Viewer_Manual/AlignSeqs|alignment page]] showing a TCoffee alignment for the selected features. '''FASTA Download Selected''' lets you download the selected sequences in aminoacid FASTA format. [[Image:EvidenceSims1.png]] [[Image:EvidenceHoverSim.png]] To change the evidence view with respect to the sorting and the filtering of the hits, you can find a little control box on top of the similarity graphics. '''Max Sims''' is the number of similarities that are listed on the page. '''Max E-Value''' filters out all similarities that have a higher E-Value than stated here. In the little combo box below these two values, you can decide to see only hits against the SEED database ('''Just FIG IDs'''), or also against other databases ('''Show all Databases'''). You can '''Sort''' the '''Results By''' ''Score'', ''Percent Identity'' (default) or ''Score per position''. These values locally refer to the hit as known from BLAST hits, so a high percent identity referring to a very small hit region can make this similarity show up as one of the first hits, as shown in the example. Checking '''Group by Genome''' will aggregate all hits to features in the same genome. A blue box will mark hits that belong to the same genome. After selecting the right values, you can press the button '''Resubmit''' to change the evidence view. [[Image:EvidenceFil1.png]] == Tabular Protein Evidence == Activate the second tab of the large page-spanning [[WebComponents/Tabview|TabView]] to see the tabular view of the evidence. You will find most of the information already shown in the visual view, presented differently and enriched with some additional information. Added are the '''Identical Proteins''' and the '''Functionally coupled''' sections, while '''Location''' information is not presented in this tab. === Similarities === The similarity [[WebComponents/Table|table]] lists hits to similar features in the SEED database (or also other databases), like described for the [[SEED_Viewer_Manual/Visual Protein Evidence|Visual Protein Evidence]]. Each row in the table represents a hit. The first column provides a checkbox to select a hit feature. Again, the buttons '''Align Selected''' and '''FASTA Download Selected''' are present and can be used to get to a TCoffee [[SEED_Viewer_Manual/AlignSeqs|alignment page]] or download the protein sequences of the selected features in FASTA format. The two buttons in the column header allow mass selection of the features. '''All''' will select all features visible in the table, '''check to last checked''' lets you select all features up to a selected feature in the [[WebComponents/Table|table]]. The ID of the hit features, as well as a link to the [[SEED_Viewer_Manual/Annotation|annotation page]] is displayed in the column '''Similar FIG Sequence'''. The next four columns describe information to the hit regions of the query and hit features ('''E-value''', '''Percent Identity''', '''Region in Query peg''' and '''Region in Similar Sequence'''). The '''Organism''' of the hit peg and its '''Function''' are shown in the next two columns. If the function is different from the function of the query feature, it is colored. Same function in the table will get the same color. '''Associated Subsystems'' of the feature are displayed in the next column. If the feature is not associated to a subsystem, you will find the text ''None added'' in the cell. There are three '''Evidence Codes''' that can be found in the last column. ''ISU'' means that the feature is unique in a cell of a subsystem. This means that there is no other feature in the genome that is thought to have the same function. ICW(number) means the feature is clustered with ''number'' features in the genome. ''FF'' says that it is in a [[Glossary#FIGfam|FIGfam]]. The [[WebComponents/Table|table]] can be exported via the button '''export table''' that can be found on top of the table. [[Image:EvidenceSims2.png]] You can filter and sort the table using the [[WebComponents/Tabview|TabView]] above the table. The second tab, '''Sims Filter''' works the same way as described for the Similarities in the [[SEED_Viewer_Manual/Evidence#Visual Protein Evidence|Visual Protein Evidence]]. The first tab '''Edit Columns''' contains a number of columns with additional information that can be added to the display of the table ([[Glossary#FIGfams|FIGfams]], different aliases to other databases and many others). Just choose a column name, press the arrow to put it into the right field and it will add it to the table. [[Image:EvidenceFilter.png]] === Domains === This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the whole length of the protein). The [[WebComponents/Table|table]] lists the '''Domain DB''' (the database for the domain that was hit), the '''ID''' in the domain database, the '''Name''' of the domain, the '''Location''' of the hit in the selected feature, the '''Score''' for the hit against the domain, as well as the '''Function''' of the domain. The table can be exported using the '''export table''' button. Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]]''' in the menu bar. [[Image:EvidenceDomTable.png]] === Identical Proteins === '''Essentially Identical Proteins''' are proteins that share a common sequence, but the start position of the proteins may vary a little. This definition was made because in different databases or close strains of organisms, it often happens that a protein is present, but the start position may be shifted in the finding genes step. So essentially, this table shows aliases of the feature that were based on protein identity. The first column of the [[WebComponents/Table|table]] shows the '''Database''' the alias can be found in, while the second column ('''ID''') offers the alias name and a link to the protein in the respective database. The following two columns describe the '''Organism''' and the '''Assignment''' for the feature for the alias. [[Image:EvidenceEIPs.png]] === Functionally Coupled === This [[WebComponent/Table|table]] lists all [[Glossary#Functional coupling|functionally coupled]] genes in the organism. You can see the '''Score''', the '''ID''' of the feature and the '''Function''' of the feature. [[Image:EvidenceFCs.png]] 1571f925ea1e959333a9dfb6a13096c36fbcae79 2097 2096 2008-11-25T13:58:44Z TobiasPaczian 17 /* Similarities */ wikitext text/x-wiki The Evidence Page is divided into two parts via a [[WebComponents/Tabview|TabView]]: The '''Visual Protein Evidence''' and the '''Tabular Protein Evidence'''. If you are logged in and the feature belongs to your private genome, this page will have additional options for you to annotate the feature. These are described [[SEED_Viewer_Manual/Editing_Capabilities/Evidence|here]]. == Visual Protein Evidence == After loading the Evidence Page, the first tab of the [[WebComponent/Tabview|TabView]] is selected. It visually shows different pre-computed tool results for the given feature. In this view, you can see evidence for ''Location'' of the product of the gene in the cell, evidence for protein ''Domains'' and evidence that show ''Similarities'' to other features. === Location === '''Location''' stand for location of the product of the feature in the cell. This section presents output for tools that look for transmembrane helices (TM) or signal peptides (SP) in the feature. In the example, you can see five transmembrane helices in the protein identified via the Phobius tool. They are visualized as little boxes, and their location on the line depicts the location of the transmembrane helices in the protein. [[Image:EvidenceLocation.png]] === Domains === This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the full length of the protein). Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]]''' in the menu bar. [[Image:EvidenceDomain.png]] === Similarities === This section graphically lists evidence for similarities to other features in the SEED and other databases. The '''E-Value Key''' shown on the top defines the colors that are used to display different E-Value ranges for the similarities to the hit features. Hovering over the E-Value Key shows the value range for each color. Each similarity is represented by two bars, showing the alignment of the similarity. The first bar is the '''query''' feature, the second the '''hit''' feature. The abbreviation in front of this bar informs you about the organism the hit feature is in. Hover over the abbreviation to get the complete organism name. To the right of the checkbox you can find the [[Glossary#Functional role|functional role]] of the hit feature. The length of the outside box shows the complete length of the respective sequence. The color of the outside box represents the range of the evalue score according to the E-Value Key bar. The length of the inner (white) box depicts the actual section of the sequence the similarity to the other feature is in. Hovering over the box will show you some information about the hit feature (see tooltip graphics below), including the [[Glossary#Functional role|functional role]], the [[Glossary#Subsystem|subsystems]] and some values describing the hit area. If you check some of the checkboxes in front of the [[Glossary#Functional role|functional role]] descriptions of the hit genes, you can access two function via the buttons on top of the Similarity graphics. The button '''Align Selected''' leads to an [[SEED_Viewer_Manual/AlignSeqs|alignment page]] showing a TCoffee alignment for the selected features. '''FASTA Download Selected''' lets you download the selected sequences in aminoacid FASTA format. [[Image:EvidenceSims1.png]] [[Image:EvidenceHoverSim.png]] To change the evidence view with respect to the sorting and the filtering of the hits, you can find a little control box on top of the similarity graphics. '''Max Sims''' is the number of similarities that are listed on the page. '''Max E-Value''' filters out all similarities that have a higher E-Value than stated here. In the little combo box below these two values, you can decide to see only hits against the SEED database ('''Just FIG IDs'''), or also against other databases ('''Show all Databases'''). You can '''Sort''' the '''Results By''' ''Score'', ''Percent Identity'' (default) or ''Score per position''. These values locally refer to the hit as known from BLAST hits, so a high percent identity referring to a very small hit region can make this similarity show up as one of the first hits, as shown in the example. Checking '''Group by Genome''' will aggregate all hits to features in the same genome. A blue box will mark hits that belong to the same genome. After selecting the right values, you can press the button '''Resubmit''' to change the evidence view. [[Image:EvidenceFil1.png]] == Tabular Protein Evidence == Activate the second tab of the large page-spanning [[WebComponents/Tabview|TabView]] to see the tabular view of the evidence. You will find most of the information already shown in the visual view, presented differently and enriched with some additional information. Added are the '''Identical Proteins''' and the '''Functionally coupled''' sections, while '''Location''' information is not presented in this tab. === Similarities === The similarity [[WebComponents/Table|table]] lists hits to similar features in the SEED database (or also other databases), like described for the [[SEED_Viewer_Manual/Visual Protein Evidence|Visual Protein Evidence]]. Each row in the table represents a hit. The first column provides a checkbox to select a hit feature. Again, the buttons '''Align Selected''' and '''FASTA Download Selected''' are present and can be used to get to a TCoffee [[SEED_Viewer_Manual/AlignSeqs|alignment page]] or download the protein sequences of the selected features in FASTA format. The two buttons in the column header allow mass selection of the features. '''All''' will select all features visible in the table, '''check to last checked''' lets you select all features up to a selected feature in the [[WebComponents/Table|table]]. The ID of the hit features, as well as a link to the [[SEED_Viewer_Manual/Annotation|annotation page]] is displayed in the column '''Similar FIG Sequence'''. The next four columns describe information to the hit regions of the query and hit features ('''E-value''', '''Percent Identity''', '''Region in Query peg''' and '''Region in Similar Sequence'''). The '''Organism''' of the hit peg and its '''Function''' are shown in the next two columns. If the function is different from the function of the query feature, it is colored. Same function in the table will get the same color. '''Associated Subsystems'' of the feature are displayed in the next column. If the feature is not associated to a subsystem, you will find the text ''None added'' in the cell. There are three '''Evidence Codes''' that can be found in the last column. ''ISU'' means that the feature is unique in a cell of a subsystem. This means that there is no other feature in the genome that is thought to have the same function. ICW(number) means the feature is clustered with ''number'' features in the genome. ''FF'' says that it is in a [[Glossary#FIGfam|FIGfam]]. The [[WebComponents/Table|table]] can be exported via the button '''export table''' that can be found on top of the table. [[Image:EvidenceSims2.png]] You can filter and sort the table using the [[WebComponents/Tabview|TabView]] above the table. The second tab, '''Sims Filter''' works the same way as described for the Similarities in the [[SEED_Viewer_Manual/Evidence#Visual Protein Evidence|Visual Protein Evidence]]. The first tab '''Edit Columns''' contains a number of columns with additional information that can be added to the display of the table ([[Glossary#FIGfams|FIGfams]], different aliases to other databases and many others). Just choose a column name, press the arrow to put it into the right field and it will add it to the table. [[Image:EvidenceFilter.png]] === Domains === This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the whole length of the protein). The [[WebComponents/Table|table]] lists the '''Domain DB''' (the database for the domain that was hit), the '''ID''' in the domain database, the '''Name''' of the domain, the '''Location''' of the hit in the selected feature, the '''Score''' for the hit against the domain, as well as the '''Function''' of the domain. The table can be exported using the '''export table''' button. Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]]''' in the menu bar. [[Image:EvidenceDomTable.png]] === Identical Proteins === '''Essentially Identical Proteins''' are proteins that share a common sequence, but the start position of the proteins may vary a little. This definition was made because in different databases or close strains of organisms, it often happens that a protein is present, but the start position may be shifted in the finding genes step. So essentially, this table shows aliases of the feature that were based on protein identity. The first column of the [[WebComponents/Table|table]] shows the '''Database''' the alias can be found in, while the second column ('''ID''') offers the alias name and a link to the protein in the respective database. The following two columns describe the '''Organism''' and the '''Assignment''' for the feature for the alias. [[Image:EvidenceEIPs.png]] === Functionally Coupled === This [[WebComponent/Table|table]] lists all [[Glossary#Functional coupling|functionally coupled]] genes in the organism. You can see the '''Score''', the '''ID''' of the feature and the '''Function''' of the feature. [[Image:EvidenceFCs.png]] 36bcb25322f27612e46edd1079b69ee7c82eb439 2098 2097 2008-11-25T13:59:49Z TobiasPaczian 17 /* Similarities */ wikitext text/x-wiki The Evidence Page is divided into two parts via a [[WebComponents/Tabview|TabView]]: The '''Visual Protein Evidence''' and the '''Tabular Protein Evidence'''. If you are logged in and the feature belongs to your private genome, this page will have additional options for you to annotate the feature. These are described [[SEED_Viewer_Manual/Editing_Capabilities/Evidence|here]]. == Visual Protein Evidence == After loading the Evidence Page, the first tab of the [[WebComponent/Tabview|TabView]] is selected. It visually shows different pre-computed tool results for the given feature. In this view, you can see evidence for ''Location'' of the product of the gene in the cell, evidence for protein ''Domains'' and evidence that show ''Similarities'' to other features. === Location === '''Location''' stand for location of the product of the feature in the cell. This section presents output for tools that look for transmembrane helices (TM) or signal peptides (SP) in the feature. In the example, you can see five transmembrane helices in the protein identified via the Phobius tool. They are visualized as little boxes, and their location on the line depicts the location of the transmembrane helices in the protein. [[Image:EvidenceLocation.png]] === Domains === This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the full length of the protein). Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]]''' in the menu bar. [[Image:EvidenceDomain.png]] === Similarities === This section graphically lists evidence for similarities to other features in the SEED and other databases. The '''E-Value Key''' shown on the top defines the colors that are used to display different E-Value ranges for the similarities to the hit features. Hovering over the E-Value Key shows the value range for each color. Each similarity is represented by two bars, showing the alignment of the similarity. The first bar is the '''query''' feature, the second the '''hit''' feature. The abbreviation in front of this bar informs you about the organism the hit feature is in. Hover over the abbreviation to get the complete organism name. To the right of the checkbox you can find the [[Glossary#Functional role|functional role]] of the hit feature. The length of the outside box shows the complete length of the respective sequence. The color of the outside box represents the range of the evalue score according to the E-Value Key bar. The length of the inner (white) box depicts the actual section of the sequence the similarity to the other feature is in. Hovering over the box will show you some information about the hit feature (see tooltip graphics below), including the [[Glossary#Functional role|functional role]], the [[Glossary#Subsystem|subsystems]] and some values describing the hit area. If you check some of the checkboxes in front of the [[Glossary#Functional role|functional role]] descriptions of the hit genes, you can access two functions via the buttons on top of the Similarity graphics. The button '''Align Selected''' leads to an [[SEED_Viewer_Manual/AlignSeqs|alignment page]] showing a TCoffee alignment for the selected features. '''FASTA Download Selected''' lets you download the selected sequences in aminoacid FASTA format. [[Image:EvidenceSims1.png]] [[Image:EvidenceHoverSim.png]] To change the evidence view with respect to the sorting and the filtering of the hits, you can find a little control box on top of the similarity graphics. '''Max Sims''' is the number of similarities that are listed on the page. '''Max E-Value''' filters out all similarities that have a higher E-Value than stated here. In the little combo box below these two values, you can decide to see only hits against the SEED database ('''Just FIG IDs'''), or also against other databases ('''Show all Databases'''). You can '''Sort''' the '''Results By''' ''Score'', ''Percent Identity'' (default) or ''Score per position''. These values locally refer to the hit as known from BLAST hits, so a high percent identity referring to a very small hit region can make this similarity show up as one of the first hits, as shown in the example. Checking '''Group by Genome''' will aggregate all hits to features in the same genome. A blue box will mark hits that belong to the same genome. After selecting the right values, you can press the button '''Resubmit''' to change the evidence view. [[Image:EvidenceFil1.png]] == Tabular Protein Evidence == Activate the second tab of the large page-spanning [[WebComponents/Tabview|TabView]] to see the tabular view of the evidence. You will find most of the information already shown in the visual view, presented differently and enriched with some additional information. Added are the '''Identical Proteins''' and the '''Functionally coupled''' sections, while '''Location''' information is not presented in this tab. === Similarities === The similarity [[WebComponents/Table|table]] lists hits to similar features in the SEED database (or also other databases), like described for the [[SEED_Viewer_Manual/Visual Protein Evidence|Visual Protein Evidence]]. Each row in the table represents a hit. The first column provides a checkbox to select a hit feature. Again, the buttons '''Align Selected''' and '''FASTA Download Selected''' are present and can be used to get to a TCoffee [[SEED_Viewer_Manual/AlignSeqs|alignment page]] or download the protein sequences of the selected features in FASTA format. The two buttons in the column header allow mass selection of the features. '''All''' will select all features visible in the table, '''check to last checked''' lets you select all features up to a selected feature in the [[WebComponents/Table|table]]. The ID of the hit features, as well as a link to the [[SEED_Viewer_Manual/Annotation|annotation page]] is displayed in the column '''Similar FIG Sequence'''. The next four columns describe information to the hit regions of the query and hit features ('''E-value''', '''Percent Identity''', '''Region in Query peg''' and '''Region in Similar Sequence'''). The '''Organism''' of the hit peg and its '''Function''' are shown in the next two columns. If the function is different from the function of the query feature, it is colored. Same function in the table will get the same color. '''Associated Subsystems'' of the feature are displayed in the next column. If the feature is not associated to a subsystem, you will find the text ''None added'' in the cell. There are three '''Evidence Codes''' that can be found in the last column. ''ISU'' means that the feature is unique in a cell of a subsystem. This means that there is no other feature in the genome that is thought to have the same function. ICW(number) means the feature is clustered with ''number'' features in the genome. ''FF'' says that it is in a [[Glossary#FIGfam|FIGfam]]. The [[WebComponents/Table|table]] can be exported via the button '''export table''' that can be found on top of the table. [[Image:EvidenceSims2.png]] You can filter and sort the table using the [[WebComponents/Tabview|TabView]] above the table. The second tab, '''Sims Filter''' works the same way as described for the Similarities in the [[SEED_Viewer_Manual/Evidence#Visual Protein Evidence|Visual Protein Evidence]]. The first tab '''Edit Columns''' contains a number of columns with additional information that can be added to the display of the table ([[Glossary#FIGfams|FIGfams]], different aliases to other databases and many others). Just choose a column name, press the arrow to put it into the right field and it will add it to the table. [[Image:EvidenceFilter.png]] === Domains === This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the whole length of the protein). The [[WebComponents/Table|table]] lists the '''Domain DB''' (the database for the domain that was hit), the '''ID''' in the domain database, the '''Name''' of the domain, the '''Location''' of the hit in the selected feature, the '''Score''' for the hit against the domain, as well as the '''Function''' of the domain. The table can be exported using the '''export table''' button. Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]]''' in the menu bar. [[Image:EvidenceDomTable.png]] === Identical Proteins === '''Essentially Identical Proteins''' are proteins that share a common sequence, but the start position of the proteins may vary a little. This definition was made because in different databases or close strains of organisms, it often happens that a protein is present, but the start position may be shifted in the finding genes step. So essentially, this table shows aliases of the feature that were based on protein identity. The first column of the [[WebComponents/Table|table]] shows the '''Database''' the alias can be found in, while the second column ('''ID''') offers the alias name and a link to the protein in the respective database. The following two columns describe the '''Organism''' and the '''Assignment''' for the feature for the alias. [[Image:EvidenceEIPs.png]] === Functionally Coupled === This [[WebComponent/Table|table]] lists all [[Glossary#Functional coupling|functionally coupled]] genes in the organism. You can see the '''Score''', the '''ID''' of the feature and the '''Function''' of the feature. [[Image:EvidenceFCs.png]] e7cf9878b6fec667c039429713fe368f6a7b544c 2100 2098 2008-11-25T14:08:11Z TobiasPaczian 17 /* Similarities */ wikitext text/x-wiki The Evidence Page is divided into two parts via a [[WebComponents/Tabview|TabView]]: The '''Visual Protein Evidence''' and the '''Tabular Protein Evidence'''. If you are logged in and the feature belongs to your private genome, this page will have additional options for you to annotate the feature. These are described [[SEED_Viewer_Manual/Editing_Capabilities/Evidence|here]]. == Visual Protein Evidence == After loading the Evidence Page, the first tab of the [[WebComponent/Tabview|TabView]] is selected. It visually shows different pre-computed tool results for the given feature. In this view, you can see evidence for ''Location'' of the product of the gene in the cell, evidence for protein ''Domains'' and evidence that show ''Similarities'' to other features. === Location === '''Location''' stand for location of the product of the feature in the cell. This section presents output for tools that look for transmembrane helices (TM) or signal peptides (SP) in the feature. In the example, you can see five transmembrane helices in the protein identified via the Phobius tool. They are visualized as little boxes, and their location on the line depicts the location of the transmembrane helices in the protein. [[Image:EvidenceLocation.png]] === Domains === This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the full length of the protein). Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]]''' in the menu bar. [[Image:EvidenceDomain.png]] === Similarities === This section graphically lists evidence for similarities to other features in the SEED and other databases. The '''E-Value Key''' shown on the top defines the colors that are used to display different E-Value ranges for the similarities to the hit features. Hovering over the E-Value Key shows the value range for each color. Each similarity is represented by two bars, showing the alignment of the similarity. The first bar is the '''query''' feature, the second the '''hit''' feature. The abbreviation in front of this bar informs you about the organism the hit feature is in. Hover over the abbreviation to get the complete organism name. To the right of the checkbox you can find the [[Glossary#Functional role|functional role]] of the hit feature. The length of the outside box shows the complete length of the respective sequence. The color of the outside box represents the range of the evalue score according to the E-Value Key bar. The length of the inner (white) box depicts the actual section of the sequence the similarity to the other feature is in. Hovering over the box will show you some information about the hit feature (see tooltip graphics below), including the [[Glossary#Functional role|functional role]], the [[Glossary#Subsystem|subsystems]] and some values describing the hit area. If you check some of the checkboxes in front of the [[Glossary#Functional role|functional role]] descriptions of the hit genes, you can access two functions via the buttons on top of the Similarity graphics. The button '''Align Selected''' leads to an [[SEED_Viewer_Manual/AlignSeqs|alignment page]] showing a TCoffee alignment for the selected features. '''FASTA Download Selected''' lets you download the selected sequences in aminoacid FASTA format. [[Image:EvidenceSims1.png]] [[Image:EvidenceHoverSim.png]] To change the evidence view with respect to the sorting and the filtering of the hits, you can find a little control box on top of the similarity graphics. '''Max Sims''' is the number of similarities that are listed on the page. '''Max E-Value''' filters out all similarities that have a higher E-Value than stated here. In the little combo box below these two values, you can decide to see only hits against the SEED database ('''Just FIG IDs'''), or also against other databases ('''Show all Databases'''). You can '''Sort''' the '''Results By''' ''Score'', ''Percent Identity'' (default) or ''Score per position''. These values locally refer to the hit as known from BLAST hits, so a high percent identity referring to a very small hit region can make this similarity show up as one of the first hits, as shown in the example. Checking '''Group by Genome''' will aggregate all hits to features in the same genome. A blue box will mark hits that belong to the same genome. After selecting the right values, you can press the button '''Resubmit''' to change the evidence view. [[Image:EvidenceFil1.png]] == Tabular Protein Evidence == Activate the second tab of the large page-spanning [[WebComponents/Tabview|TabView]] to see the tabular view of the evidence. You will find most of the information already shown in the visual view, presented differently and enriched with some additional information. Added are the '''Identical Proteins''' and the '''Functionally coupled''' sections, while '''Location''' information is not presented in this tab. === Similarities === The similarity [[WebComponents/Table|table]] lists hits to similar features in the SEED and other databases, as described at [[SEED_Viewer_Manual/Visual Protein Evidence|Visual Protein Evidence]]. Each row in the table represents a hit. The first column provides a checkbox to select a hit feature. Again, the buttons '''Align Selected''' and '''FASTA Download Selected''' are present and can be used to get to a TCoffee [[SEED_Viewer_Manual/AlignSeqs|alignment page]] or download the protein sequences of the selected features in FASTA format. The two buttons in the column header allow mass selection of the features. '''All''' will select all features visible in the table, '''check to last checked''' lets you select all features up to a selected feature in the [[WebComponents/Table|table]]. The ID of the hit features, as well as a link to the [[SEED_Viewer_Manual/Annotation|annotation page]] is displayed in the column '''Similar FIG Sequence'''. The next four columns describe information to the hit regions of the query and hit features ('''E-value''', '''Percent Identity''', '''Region in Query peg''' and '''Region in Similar Sequence'''). The '''Organism''' of the hit peg and its '''Function''' are shown in the next two columns. If the function is different from the function of the query feature, it is colored. Same function in the table will get the same color. '''Associated Subsystems'' of the feature are displayed in the next column. If the feature is not associated to a subsystem, you will find the text ''None added'' in the cell. There are three '''Evidence Codes''' that can be found in the last column. ''ISU'' means that the feature is unique in a cell of a subsystem. This means that there is no other feature in the genome that is thought to have the same function. ICW(number) means the feature is clustered with ''number'' features in the genome. ''FF'' says that it is in a [[Glossary#FIGfam|FIGfam]]. The [[WebComponents/Table|table]] can be exported via the button '''export table''' that can be found on top of the table. [[Image:EvidenceSims2.png]] You can filter and sort the table using the [[WebComponents/Tabview|TabView]] above the table. The second tab, '''Sims Filter''' works the same way as described for the Similarities in the [[SEED_Viewer_Manual/Evidence#Visual Protein Evidence|Visual Protein Evidence]]. The first tab '''Edit Columns''' contains a number of columns with additional information that can be added to the display of the table ([[Glossary#FIGfams|FIGfams]], different aliases to other databases and many others). Just choose a column name, press the arrow to put it into the right field and it will add it to the table. [[Image:EvidenceFilter.png]] === Domains === This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the whole length of the protein). The [[WebComponents/Table|table]] lists the '''Domain DB''' (the database for the domain that was hit), the '''ID''' in the domain database, the '''Name''' of the domain, the '''Location''' of the hit in the selected feature, the '''Score''' for the hit against the domain, as well as the '''Function''' of the domain. The table can be exported using the '''export table''' button. Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]]''' in the menu bar. [[Image:EvidenceDomTable.png]] === Identical Proteins === '''Essentially Identical Proteins''' are proteins that share a common sequence, but the start position of the proteins may vary a little. This definition was made because in different databases or close strains of organisms, it often happens that a protein is present, but the start position may be shifted in the finding genes step. So essentially, this table shows aliases of the feature that were based on protein identity. The first column of the [[WebComponents/Table|table]] shows the '''Database''' the alias can be found in, while the second column ('''ID''') offers the alias name and a link to the protein in the respective database. The following two columns describe the '''Organism''' and the '''Assignment''' for the feature for the alias. [[Image:EvidenceEIPs.png]] === Functionally Coupled === This [[WebComponent/Table|table]] lists all [[Glossary#Functional coupling|functionally coupled]] genes in the organism. You can see the '''Score''', the '''ID''' of the feature and the '''Function''' of the feature. [[Image:EvidenceFCs.png]] 28d46f1d16f66d228343501dc8863d290ecaa94a 6 1516 2082 2008-11-25T11:47:34Z DanielaBartels 10 wikitext text/x-wiki da39a3ee5e6b4b0d3255bfef95601890afd80709 0 1463 2095 1918 2008-11-25T13:56:53Z DanielaBartels 10 /* (4) Body of the Page */ wikitext text/x-wiki The SEED is a framework to support comparative analysis and annotation of genomes. The SEED Viewer allows you to explore the curated genomes that have been produced by a cooperative effort that includes Fellowship for Interpretation of Genomes (FIG), Argonne National Laboratory, the University of Chicago and teams from a number of other institutions. These pages will cover the usage of the different pages within the Seed Viewer. An overview of the main pages in the SeedViewer can be found in the '''[[SEED_Viewer_Manual/Contents|Contents Page]]'''. == Home == The home page of the seedviewer offers you several entry points to explore the data in the [[Home_of_the_SEED|SEED]]. Common components of a web page in the seedviewer are the following. The image below depicts the locations of the components: === (1) [[SEED_Viewer_Manual/Menu|The menu]] === Hovering over the menu will show you submenus that are relevant for the page you are viewing. The categories '''[[SEED_Viewer_Manual/Menu#Navigate_Menu|Navigate]]''' and '''[[SEED_Viewer_Manual/Menu#Help_Menu|Help]]''' will always be present on each page. Other menu categories are added dependent on the context of the page. Click [[SEED_Viewer_Manual/Menu|here]] to learn more about using the menu. === (2) [[SEED_Viewer_Manual/Find|Find Window]] === The Find window allows you to search for keywords or ids. To learn more about the find window, click [[SEED_Viewer_Manual/Find|here]]. === (3) [[WebComponents/Login|Login Box]] === Some actions may require a user to get a user account and log in. This is necessary for viewing private organisms a user has uploaded to the [[RAST_Tutorial|RAST]]. You can create a login by clicking on '''Register''' in the '''Help''' menu. To learn more about user management click [[SEED_Viewer_Manual/UserManagement|here]]. === (4) Body of the Page === The home page allows you to specifically search the SEED data using five categories. They are presented in a [[WebComponents/Tabview|TabView]] at the bottom of the Home page: '''a) Organisms''' Select an organism of interest in the [[SEED_Viewer_Manual/OrganismSelect|Organism Select]] and press the button '''select'''. This will lead to the [[SEED_Viewer_Manual/OrganismPage|Organism Page]] of that organism. '''b) Subsystems''' Selecting a subsystem in the Select Box and clicking '''Select''' will lead you to a [[SEED_Viewer_Manual/Subsystems|Subsystem Page]]. You can narrow the selection by typing in a part of the subsystem name into the field on top of the select box. '''c) ID search''' If you know the ID of a gene or protein you're interested in, you can directly type it into this field and press '''ID Search'''. The ID can be a SEED (fig) id as well as many other types of IDs from other databases (e.g. GenBank, KEGG, SwissProt, UniProt and others). These IDs are saved in the SEED as [[Aliases|Aliases]]. '''d) Text search''' You can search for any type of data in this field. This includes search for Organisms, Subsystems, IDs as well as Functional Roles of proteins. It should be used carefully, as the search is an infix search and can take very long (e.g. if you only type in one letter it may take forever). If you already know that you are looking for, e.g. a subsystem, it would be faster to use the Subsystems tab. '''e) BLAST''' This tab offers the option to search a DNA or protein sequence against an organism in the SEED. It is described in more detail [[SEED_Viewer_Manual/BLASTOrganism|here]]. [[Image:Home1.png]] 1db337403d6399e1a40fdafb44820db513f8a844 0 1478 2099 2031 2008-11-25T14:00:54Z DanielaBartels 10 /* Menu Overview */ wikitext text/x-wiki == Menu Overview == The menu is a small bar below the logo of each page. Most menus have submenus that can be accessed via hovering over the menu. Right-click the submenu you want to go to. If no submenu is present, you can directly click the menu itself. === Navigate Menu === This menu is present on every SeedViewer page. The first entry '''Startpage''' will lead to the SeedViewer [[SEED_Viewer_Manual|HomePage]]. '''Organisms''' will open the [[SEED_Viewer_Manual/OrganismSelect|Organism Select]] page. You will see an overview of all organisms in the SEED and are able to select one to view in detail. '''Subsystems''' will do the same for subsystems. '''FIGFams''' leads to an entry point for browsing [[SEED_Viewer_Manual/FIGfams|FIGfams]]. You can find more information about FIGfams [[Glossary#FIGfam|here]]. The '''BLAST Search''' links to the [[SEED_Viewer_Manual/BLASTOrganism|BLAST Page]]. You will be able to BLAST a sequence against an organism in the SEED. [[Image:MenuNav.png]] === Help Menu === This menu is also present on all SeedViewer pages. The first link '''What is the SEED''' will lead you to the [[Home_of_the_SEED|SEED Homepage]]. Clicking the second link '''How to use the SEED Viewer''' will get you to this wiki. '''Submitting data to SEED''' lets you browse the [[RAST_Tutorial|RAST Tutorial]]. '''Contact''' enables you to write an email to the SEED team. Clicking '''Register''' is the first step to get a user account. It will lead to the [[SEED_Viewer_Manual/Register|Register]] page. '''I forgot my password''' enables you to [[SEED_Viewer_Manual/RequestNewPassword|Request a new password]]. [[Image:MenuHelp.png]] === Organism Menu === In the context of a selected organism, an organism menu will appear. '''General Information''' will lead to the [[SEED_Viewer_Manual/OrganismPage|Organism Page]] of the selected organism. The '''Feature Table''' will open the [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] and show you the features present in that organism. '''Genome Browser''' leads to the [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] for the selected organism. Clicking '''Scenarios''' shows the [[SEED_Viewer_Manual/Scenarios|Scenarios]] page for your organism. '''Subsystems''' opens a page that lets you select subsystems. '''Export''' enables you to [[SEED_Viewer_Manual/Export|download]] the features of your organism. [[Image:MenuOrganism.png]] === Comparative Tools === This menu is also present whenever an organism is viewed. Different kinds of comparisons of your selected organism to other organisms are available here. '''Function based Comparison''' - The [[SEED_Viewer_Manual/CompareMetabolicReconstruction|Compare Metabolic Reconstruction]] will enable you to see the metabolic reconstruction of your selected organism against that of another one. The '''Sequence based Comparison''' [[SEED_Viewer_Manual/MultiGenomeCompare|Multi Genome Compare]] shows a table and a graphics comparing a selected set of organisms projected against your chosen one (BLAST-based). Use the '''KEGG Metabolic Analysis''' [[SEED_Viewer_Manual/KEGG|to project the metabolic capabilities]] of your organism on KEGG maps. Blasting against your organism is enabled using the '''[[SEED_Viewer_Manual/BLASTOrganism|BLAST Search]]'''. [[Image:CompTools.png]] === Feature Menu === Whenever a feature is defined on a SeedViewer page, you will find the '''Feature''' menu for that feature. The '''Feature Overview''' points to the [[SEED_Viewer_Manual/Annotation|Annotation]] page. It shows general information about the feature, als well as a Compare Regions View that displays the feature in its genomic context and in comparison to homologs in other genomes. '''DNA Sequence''' will open a page with the DNA Sequence of the feature (in FASTA format). '''DNA w/ flanking''' not only prints the DNA sequence of the feature, but also includes a user-defined number of bases upstream and downstream of the feature. '''Protein Sequence''' will show you the protein FASTA sequence (translated from the DNA sequence) of the feature. '''Feature Evidence vs. FIG''' and '''Feature Evidence vs. all DB''' link to the [[SEED_Viewer_Manual/Evidence|Evidence]] page. The difference between the two is that the evidence shown for the feature includes only evidence against features in the SEED or also against other databases (e.g. GenBank, SwissProt, UniProt and many others). The evidence page will also allow you to make this selection or change it there. [[Image:MenuFeature.png]] === Feature Tools === This menu is also present if a feature is defined. It lets the user run a variaty of tools using the feature sequence. These include tools that look for transmembrane helices (e.t. TMHMM), signal peptides (PSORT, SignalP), protein domains (e.g. InterPro, ProDom) and others. [[Image:MenuFeatTools.png]] === FIGfams Menu === On SeedViewer pages that deal with [[Glossary#FIGfam|FIGfams]], you will find an additional FIGfams menu. The '''Home''' link leads to the entry page to [[SEED_Viewer_Manual/FIGfams|FIGfams]]. The '''Release History''' will lead you to a [[SEED_Viewer_Manual/FIGfamsRelease|page]] containing a number of statistics about the current release of the FIGfams. '''Download''' will connect you to the FTP server to enable you to download the FIGfams. [[Image:MenuFIGfam.png]] 009ffb533d51816e0bc66f4570f7ff767d7809af 0 1517 2101 2008-11-25T14:23:40Z DanielaBartels 10 wikitext text/x-wiki == Subsystems == === Diagram === [[Image:SubsystemDiagram.png]] === Functional Roles === [[Image:SubsystemFRs.png]] === Spreadsheet === [[Image:SubsystemSpreadsh.png]] === Description === === Additional Notes === a2f4376a5e771973002024b46cc70845fcb0b67a 2105 2101 2008-11-25T14:34:24Z DanielaBartels 10 /* Spreadsheet */ wikitext text/x-wiki == Subsystems == === Diagram === [[Image:SubsystemDiagram.png]] === Functional Roles === [[Image:SubsystemFRs.png]] === Spreadsheet === [[Image:SubsystemSpreadsheet.png]] === Description === === Additional Notes === 4f058f431e257f44c5f2994df4200ca8dfb8569a 2107 2105 2008-11-25T14:52:55Z DanielaBartels 10 /* Subsystems */ wikitext text/x-wiki == Subsystems == A [[Glossary#Subsystem|subsystem]] is a collection of [[Glossary#Functional role|functional roles]] that are associated to each other in a system. Such a system can be a metabolic pathway, a component if a cell like a secretion system and others. The subsystem page in the SeedViewer is divided into different parts via a [[WebComponent/Tabview|TabView]]. The TabView can consist of 3-5 tabs. The first tab shows a '''Diagram''' of the subsystem, the second tab displays a [[WebComponents/Table|table]] with the '''Functional Roles''' present in the subsystem. The '''Spreadsheet''' showing relating the functional roles in the subsystem to features in genomes can be found in the third tab. === Diagram === [[Image:SubsystemDiagram.png]] === Functional Roles === [[Image:SubsystemFRs.png]] === Spreadsheet === [[Image:SubsystemSpreadsheet.png]] === Description === === Additional Notes === fcbd7c7376ef8b363baaa2ee41c2df6f6e1fc1a3 2108 2107 2008-11-25T15:11:11Z DanielaBartels 10 /* Subsystems */ wikitext text/x-wiki == Subsystems == A [[Glossary#Subsystem|subsystem]] is a collection of [[Glossary#Functional role|functional roles]] that are associated to each other in a system. Such a system can be a metabolic pathway, a component if a cell like a secretion system and others. The subsystem page in the SeedViewer is divided into different parts via a [[WebComponent/Tabview|TabView]]. The TabView can consist of 3-5 tabs. The first tab shows a '''Diagram''' of the subsystem, the second tab displays a [[WebComponents/Table|table]] with the '''Functional Roles''' present in the subsystem. The '''Spreadsheet''' showing relating the functional roles in the subsystem to features in genomes can be found in the third tab. The fourth and fifth tab show a description and additional notes to a subsystem. They only appear if a subsystem has a description / notes. === Diagram === The subsystem diagram shows the connections between the functional roles in a subsystem. The boxes represent the functional roles via their abbreviations. The circles are connecting intermediates, that are described in the table which is part of the diagram. [[Image:SubsystemDiagram.png]] === Functional Roles === [[Image:SubsystemFRs.png]] === Spreadsheet === [[Image:SubsystemSpreadsheet.png]] === Description === === Additional Notes === d2058f9ad1ea3897f0c2dc3f16ab603ba0304cfb 2109 2108 2008-11-25T15:23:15Z DanielaBartels 10 /* Diagram */ wikitext text/x-wiki == Subsystems == A [[Glossary#Subsystem|subsystem]] is a collection of [[Glossary#Functional role|functional roles]] that are associated to each other in a system. Such a system can be a metabolic pathway, a component if a cell like a secretion system and others. The subsystem page in the SeedViewer is divided into different parts via a [[WebComponent/Tabview|TabView]]. The TabView can consist of 3-5 tabs. The first tab shows a '''Diagram''' of the subsystem, the second tab displays a [[WebComponents/Table|table]] with the '''Functional Roles''' present in the subsystem. The '''Spreadsheet''' showing relating the functional roles in the subsystem to features in genomes can be found in the third tab. The fourth and fifth tab show a description and additional notes to a subsystem. They only appear if a subsystem has a description / notes. === Diagram === The subsystem diagram shows the connections between the functional roles in a subsystem. The boxes represent the functional roles via their abbreviations. The circles are connecting intermediates, that are described in the table which is part of the diagram. The functional roles in the diagram can be colored according to their presence in a genome. Click the button '''Color Diagram''' to get a combo box with all genomes in the subsystem. Select your genome of interest and press '''do coloring'''. The boxes for the functional roles defined for that genome will now be colored in green. [[Image:SubsystemDiagram.png]] === Functional Roles === [[Image:SubsystemFRs.png]] === Spreadsheet === [[Image:SubsystemSpreadsheet.png]] === Description === === Additional Notes === 5bc21aaeed5dcc88984e087f8164f2622cc6929b 2110 2109 2008-11-25T15:58:48Z DanielaBartels 10 /* Functional Roles */ wikitext text/x-wiki == Subsystems == A [[Glossary#Subsystem|subsystem]] is a collection of [[Glossary#Functional role|functional roles]] that are associated to each other in a system. Such a system can be a metabolic pathway, a component if a cell like a secretion system and others. The subsystem page in the SeedViewer is divided into different parts via a [[WebComponent/Tabview|TabView]]. The TabView can consist of 3-5 tabs. The first tab shows a '''Diagram''' of the subsystem, the second tab displays a [[WebComponents/Table|table]] with the '''Functional Roles''' present in the subsystem. The '''Spreadsheet''' showing relating the functional roles in the subsystem to features in genomes can be found in the third tab. The fourth and fifth tab show a description and additional notes to a subsystem. They only appear if a subsystem has a description / notes. === Diagram === The subsystem diagram shows the connections between the functional roles in a subsystem. The boxes represent the functional roles via their abbreviations. The circles are connecting intermediates, that are described in the table which is part of the diagram. The functional roles in the diagram can be colored according to their presence in a genome. Click the button '''Color Diagram''' to get a combo box with all genomes in the subsystem. Select your genome of interest and press '''do coloring'''. The boxes for the functional roles defined for that genome will now be colored in green. [[Image:SubsystemDiagram.png]] === Functional Roles === This [[WebComponents/Table|table]] lists all functional roles present in the subsystem. The first column shows '''Group Aliases''' for the functional role. Functional roles can be aggregated in groups (subsets). Subset names that start with a '*' contain alternative ways to implement a function. The abbreviation ('''Abbrev.''') for a functional role must be unique for the functional roles in the subsystem. They are used in different displays like the Diagram or the Speadsheet. The third column lists the full name of the functional role. EC-Numbers are often part of the functional role (for enzymes), and are stated in parentheses after the name of the functional role. The following two columns deal with reactions a functional role is connected to. Clicking on the link opens a new window showing the KEGG reaction. Next to annotator-curated KEGG reactions, we show the KEGG reactions of the curation effort of the Hope College team that collaborate with the SEED. GeneOntology (GO) links are displayed in the next column. The links point to the GO-number in GeneOntology's Amigo-Tool. [[Image:SubsystemFRs.png]] === Spreadsheet === [[Image:SubsystemSpreadsheet.png]] === Description === === Additional Notes === 649fec67c609acf4779692f0d0db7122369b2e7e 2111 2110 2008-11-25T16:01:22Z DanielaBartels 10 /* Functional Roles */ wikitext text/x-wiki == Subsystems == A [[Glossary#Subsystem|subsystem]] is a collection of [[Glossary#Functional role|functional roles]] that are associated to each other in a system. Such a system can be a metabolic pathway, a component if a cell like a secretion system and others. The subsystem page in the SeedViewer is divided into different parts via a [[WebComponent/Tabview|TabView]]. The TabView can consist of 3-5 tabs. The first tab shows a '''Diagram''' of the subsystem, the second tab displays a [[WebComponents/Table|table]] with the '''Functional Roles''' present in the subsystem. The '''Spreadsheet''' showing relating the functional roles in the subsystem to features in genomes can be found in the third tab. The fourth and fifth tab show a description and additional notes to a subsystem. They only appear if a subsystem has a description / notes. === Diagram === The subsystem diagram shows the connections between the functional roles in a subsystem. The boxes represent the functional roles via their abbreviations. The circles are connecting intermediates, that are described in the table which is part of the diagram. The functional roles in the diagram can be colored according to their presence in a genome. Click the button '''Color Diagram''' to get a combo box with all genomes in the subsystem. Select your genome of interest and press '''do coloring'''. The boxes for the functional roles defined for that genome will now be colored in green. [[Image:SubsystemDiagram.png]] === Functional Roles === This [[WebComponents/Table|table]] lists all functional roles present in the subsystem. The first column shows '''Group Aliases''' for the functional role. Functional roles can be aggregated in groups (subsets). Subset names that start with a '*' contain alternative ways to implement a function. The abbreviation ('''Abbrev.''') for a functional role must be unique for the functional roles in the subsystem. They are used in different displays like the Diagram or the Speadsheet. The third column lists the full name of the functional role. EC-Numbers are often part of the functional role (for enzymes), and are stated in parentheses after the name of the functional role. The following two columns deal with reactions a functional role is connected to. Clicking on the link opens a new window showing the KEGG reaction. Next to annotator-curated KEGG reactions, we show the KEGG reactions of the curation effort of the [[SEED_People/Hope College|Hope College]] team that collaborates with the SEED. GeneOntology (GO) links are displayed in the next column. The links point to the GO-number in GeneOntology's Amigo-Tool. [[Image:SubsystemFRs.png]] === Spreadsheet === [[Image:SubsystemSpreadsheet.png]] === Description === === Additional Notes === 2f6690751524a85b405a15179f0d8e8e63a4a964 2112 2111 2008-11-25T16:01:44Z DanielaBartels 10 /* Functional Roles */ wikitext text/x-wiki == Subsystems == A [[Glossary#Subsystem|subsystem]] is a collection of [[Glossary#Functional role|functional roles]] that are associated to each other in a system. Such a system can be a metabolic pathway, a component if a cell like a secretion system and others. The subsystem page in the SeedViewer is divided into different parts via a [[WebComponent/Tabview|TabView]]. The TabView can consist of 3-5 tabs. The first tab shows a '''Diagram''' of the subsystem, the second tab displays a [[WebComponents/Table|table]] with the '''Functional Roles''' present in the subsystem. The '''Spreadsheet''' showing relating the functional roles in the subsystem to features in genomes can be found in the third tab. The fourth and fifth tab show a description and additional notes to a subsystem. They only appear if a subsystem has a description / notes. === Diagram === The subsystem diagram shows the connections between the functional roles in a subsystem. The boxes represent the functional roles via their abbreviations. The circles are connecting intermediates, that are described in the table which is part of the diagram. The functional roles in the diagram can be colored according to their presence in a genome. Click the button '''Color Diagram''' to get a combo box with all genomes in the subsystem. Select your genome of interest and press '''do coloring'''. The boxes for the functional roles defined for that genome will now be colored in green. [[Image:SubsystemDiagram.png]] === Functional Roles === This [[WebComponents/Table|table]] lists all functional roles present in the subsystem. The first column shows '''Group Aliases''' for the functional role. Functional roles can be aggregated in groups (subsets). Subset names that start with a '*' contain alternative ways to implement a function. The abbreviation ('''Abbrev.''') for a functional role must be unique for the functional roles in the subsystem. They are used in different displays like the Diagram or the Speadsheet. The third column lists the full name of the functional role. EC-Numbers are often part of the functional role (for enzymes), and are stated in parentheses after the name of the functional role. The following two columns deal with reactions a functional role is connected to. Clicking on the link opens a new window showing the KEGG reaction. Next to annotator-curated KEGG reactions, we show the KEGG reactions of the curation effort of the [[SEED_People#Hope College|Hope College]] team that collaborates with the SEED. GeneOntology (GO) links are displayed in the next column. The links point to the GO-number in GeneOntology's Amigo-Tool. [[Image:SubsystemFRs.png]] === Spreadsheet === [[Image:SubsystemSpreadsheet.png]] === Description === === Additional Notes === 1d87b1d7e3dbd0f163e2bc57440acd4fbaa427e5 2113 2112 2008-11-25T16:03:32Z DanielaBartels 10 /* Functional Roles */ wikitext text/x-wiki == Subsystems == A [[Glossary#Subsystem|subsystem]] is a collection of [[Glossary#Functional role|functional roles]] that are associated to each other in a system. Such a system can be a metabolic pathway, a component if a cell like a secretion system and others. The subsystem page in the SeedViewer is divided into different parts via a [[WebComponent/Tabview|TabView]]. The TabView can consist of 3-5 tabs. The first tab shows a '''Diagram''' of the subsystem, the second tab displays a [[WebComponents/Table|table]] with the '''Functional Roles''' present in the subsystem. The '''Spreadsheet''' showing relating the functional roles in the subsystem to features in genomes can be found in the third tab. The fourth and fifth tab show a description and additional notes to a subsystem. They only appear if a subsystem has a description / notes. === Diagram === The subsystem diagram shows the connections between the functional roles in a subsystem. The boxes represent the functional roles via their abbreviations. The circles are connecting intermediates, that are described in the table which is part of the diagram. The functional roles in the diagram can be colored according to their presence in a genome. Click the button '''Color Diagram''' to get a combo box with all genomes in the subsystem. Select your genome of interest and press '''do coloring'''. The boxes for the functional roles defined for that genome will now be colored in green. [[Image:SubsystemDiagram.png]] === Functional Roles === This [[WebComponents/Table|table]] lists all functional roles present in the subsystem. The first column shows '''Group Aliases''' for the functional role. Functional roles can be aggregated in groups (subsets). Subset names that start with a '*' contain alternative ways to implement a function. The abbreviation ('''Abbrev.''') for a functional role must be unique for the functional roles in the subsystem. They are used in different displays like the Diagram or the Speadsheet. The third column lists the full name of the functional role. EC-Numbers are often part of the functional role (for enzymes), and are stated in parentheses after the name of the functional role. The following two columns deal with reactions a functional role is connected to. Clicking on the link opens a new window showing the KEGG reaction. Next to annotator-curated KEGG reactions, we show the KEGG reactions of the curation effort of the [[SEED_People#Hope College|Hope College]] team that collaborates with the SEED. GeneOntology (GO) links are displayed in the next column. The links point to the GO-number in GeneOntology's Amigo-Tool. The last column can contain literature (PubMed IDs) that describes the functional role in detail. If present, you will find a link to PubMed in this column. [[Image:SubsystemFRs.png]] === Spreadsheet === [[Image:SubsystemSpreadsheet.png]] === Description === === Additional Notes === dd04b88b55cbfe7b4833ce84c03cac6821e4680d 2114 2113 2008-11-25T16:19:27Z DanielaBartels 10 /* Spreadsheet */ wikitext text/x-wiki == Subsystems == A [[Glossary#Subsystem|subsystem]] is a collection of [[Glossary#Functional role|functional roles]] that are associated to each other in a system. Such a system can be a metabolic pathway, a component if a cell like a secretion system and others. The subsystem page in the SeedViewer is divided into different parts via a [[WebComponent/Tabview|TabView]]. The TabView can consist of 3-5 tabs. The first tab shows a '''Diagram''' of the subsystem, the second tab displays a [[WebComponents/Table|table]] with the '''Functional Roles''' present in the subsystem. The '''Spreadsheet''' showing relating the functional roles in the subsystem to features in genomes can be found in the third tab. The fourth and fifth tab show a description and additional notes to a subsystem. They only appear if a subsystem has a description / notes. === Diagram === The subsystem diagram shows the connections between the functional roles in a subsystem. The boxes represent the functional roles via their abbreviations. The circles are connecting intermediates, that are described in the table which is part of the diagram. The functional roles in the diagram can be colored according to their presence in a genome. Click the button '''Color Diagram''' to get a combo box with all genomes in the subsystem. Select your genome of interest and press '''do coloring'''. The boxes for the functional roles defined for that genome will now be colored in green. [[Image:SubsystemDiagram.png]] === Functional Roles === This [[WebComponents/Table|table]] lists all functional roles present in the subsystem. The first column shows '''Group Aliases''' for the functional role. Functional roles can be aggregated in groups (subsets). Subset names that start with a '*' contain alternative ways to implement a function. The abbreviation ('''Abbrev.''') for a functional role must be unique for the functional roles in the subsystem. They are used in different displays like the Diagram or the Speadsheet. The third column lists the full name of the functional role. EC-Numbers are often part of the functional role (for enzymes), and are stated in parentheses after the name of the functional role. The following two columns deal with reactions a functional role is connected to. Clicking on the link opens a new window showing the KEGG reaction. Next to annotator-curated KEGG reactions, we show the KEGG reactions of the curation effort of the [[SEED_People#Hope College|Hope College]] team that collaborates with the SEED. GeneOntology (GO) links are displayed in the next column. The links point to the GO-number in GeneOntology's Amigo-Tool. The last column can contain literature (PubMed IDs) that describes the functional role in detail. If present, you will find a link to PubMed in this column. [[Image:SubsystemFRs.png]] === Spreadsheet === The subsystem spreadsheet displays the features that are assigned with the functional roles in all organisms that are part of the subsystem. The organisms are displayed in the first column. The links lead to the [[SEED_Viewer_Manual/OrganismPage|Organism Page]]. [[Image:SubsystemSpreadsheet.png]] === Description === === Additional Notes === f0edffa469490373b0d7280d978e1933cab4bcaa 2115 2114 2008-11-25T16:30:37Z DanielaBartels 10 wikitext text/x-wiki == Subsystems == A [[Glossary#Subsystem|subsystem]] is a collection of [[Glossary#Functional role|functional roles]] that are associated to each other in a system. Such a system can be a metabolic pathway, a component if a cell like a secretion system and others. The subsystem page in the SeedViewer is divided into different parts via a [[WebComponent/Tabview|TabView]]. The TabView can consist of 3-5 tabs. The first tab shows a '''Diagram''' of the subsystem, the second tab displays a [[WebComponents/Table|table]] with the '''Functional Roles''' present in the subsystem. The '''Spreadsheet''' showing relating the functional roles in the subsystem to features in genomes can be found in the third tab. The fourth and fifth tab show a description and additional notes to a subsystem. They only appear if a subsystem has a description / notes. === Diagram === The subsystem diagram shows the connections between the functional roles in a subsystem. The boxes represent the functional roles via their abbreviations. The circles are connecting intermediates, that are described in the table which is part of the diagram. The functional roles in the diagram can be colored according to their presence in a genome. Click the button '''Color Diagram''' to get a combo box with all genomes in the subsystem. Select your genome of interest and press '''do coloring'''. The boxes for the functional roles defined for that genome will now be colored in green. [[Image:SubsystemDiagram.png]] === Functional Roles === This [[WebComponents/Table|table]] lists all functional roles present in the subsystem. The first column shows '''Group Aliases''' for the functional role. Functional roles can be aggregated in groups (subsets). Subset names that start with a '*' contain alternative ways to implement a function. The abbreviation ('''Abbrev.''') for a functional role must be unique for the functional roles in the subsystem. They are used in different displays like the Diagram or the Speadsheet. The third column lists the full name of the functional role. EC-Numbers are often part of the functional role (for enzymes), and are stated in parentheses after the name of the functional role. The following two columns deal with reactions a functional role is connected to. Clicking on the link opens a new window showing the KEGG reaction. Next to annotator-curated KEGG reactions, we show the KEGG reactions of the curation effort of the [[SEED_People#Hope College|Hope College]] team that collaborates with the SEED. GeneOntology (GO) links are displayed in the next column. The links point to the GO-number in GeneOntology's Amigo-Tool. The last column can contain literature (PubMed IDs) that describes the functional role in detail. If present, you will find a link to PubMed in this column. [[Image:SubsystemFRs.png]] === Spreadsheet === The subsystem spreadsheet displays the features that are assigned with the functional roles in all organisms that are part of the subsystem. The organisms are displayed in the first column. The links lead to the [[SEED_Viewer_Manual/OrganismPage|Organism Page]]. The column header includes a filter option for the organism, doing an infix search on the organism name. The '''Domain''' (Bacterial, Archaeal or Eukaryote) of the organism is shown in the second column. For each organism in the spreadsheet, a '''Variant Code''' is assigned. Usually, there is more than one way to fulfill a subsystem. Metabolic pathways can have alternatives, or parts of the pathway may be present or absent in an organism. [[[Glossary/Variant Code|Variant Codes]] are assigned to the organism to express this behavior. There are two special Variant Codes: '''0''' and '''-1'''. The Variant Code '''-1''' means that the organism has no active variant in this subsystem, meaning it does not implement the subsystem. '''0''' means that the curator has not yet assigned a variant to the genome. Due to the flow of newly sequenced genomes into the SEED, this variant code may show up sometimes. [[Image:SubsystemSpreadsheet.png]] === Description === === Additional Notes === 99b419dae06824bd5365087bb20541144f3b2463 2116 2115 2008-11-25T16:36:08Z DanielaBartels 10 /* Spreadsheet */ wikitext text/x-wiki == Subsystems == A [[Glossary#Subsystem|subsystem]] is a collection of [[Glossary#Functional role|functional roles]] that are associated to each other in a system. Such a system can be a metabolic pathway, a component if a cell like a secretion system and others. The subsystem page in the SeedViewer is divided into different parts via a [[WebComponent/Tabview|TabView]]. The TabView can consist of 3-5 tabs. The first tab shows a '''Diagram''' of the subsystem, the second tab displays a [[WebComponents/Table|table]] with the '''Functional Roles''' present in the subsystem. The '''Spreadsheet''' showing relating the functional roles in the subsystem to features in genomes can be found in the third tab. The fourth and fifth tab show a description and additional notes to a subsystem. They only appear if a subsystem has a description / notes. === Diagram === The subsystem diagram shows the connections between the functional roles in a subsystem. The boxes represent the functional roles via their abbreviations. The circles are connecting intermediates, that are described in the table which is part of the diagram. The functional roles in the diagram can be colored according to their presence in a genome. Click the button '''Color Diagram''' to get a combo box with all genomes in the subsystem. Select your genome of interest and press '''do coloring'''. The boxes for the functional roles defined for that genome will now be colored in green. [[Image:SubsystemDiagram.png]] === Functional Roles === This [[WebComponents/Table|table]] lists all functional roles present in the subsystem. The first column shows '''Group Aliases''' for the functional role. Functional roles can be aggregated in groups (subsets). Subset names that start with a '*' contain alternative ways to implement a function. The abbreviation ('''Abbrev.''') for a functional role must be unique for the functional roles in the subsystem. They are used in different displays like the Diagram or the Speadsheet. The third column lists the full name of the functional role. EC-Numbers are often part of the functional role (for enzymes), and are stated in parentheses after the name of the functional role. The following two columns deal with reactions a functional role is connected to. Clicking on the link opens a new window showing the KEGG reaction. Next to annotator-curated KEGG reactions, we show the KEGG reactions of the curation effort of the [[SEED_People#Hope College|Hope College]] team that collaborates with the SEED. GeneOntology (GO) links are displayed in the next column. The links point to the GO-number in GeneOntology's Amigo-Tool. The last column can contain literature (PubMed IDs) that describes the functional role in detail. If present, you will find a link to PubMed in this column. [[Image:SubsystemFRs.png]] === Spreadsheet === The subsystem spreadsheet displays the features that are assigned with the functional roles in all organisms that are part of the subsystem. The organisms are displayed in the first column. The links lead to the [[SEED_Viewer_Manual/OrganismPage|Organism Page]]. The column header includes a filter option for the organism, doing an infix search on the organism name. The '''Domain''' (Bacterial, Archaeal or Eukaryote) of the organism is shown in the second column. For each organism in the spreadsheet, a '''Variant Code''' is assigned. Usually, there is more than one way to fulfill a subsystem. Metabolic pathways can have alternatives, or parts of the pathway may be present or absent in an organism. [[[Glossary/Variant Code|Variant Codes]] are assigned to the organism to express this behavior. There are two special Variant Codes: '''0''' and '''-1'''. The Variant Code '''-1''' means that the organism has no active variant in this subsystem, meaning it does not implement the subsystem. '''0''' means that the curator has not yet assigned a variant to the genome. Due to the flow of newly sequenced genomes into the SEED, this variant code may show up sometimes. The next column is used to filter active or not active variants. If you want to see only the active ones (default), print '''yes''' into the filter in the column header. For seeing only the not active ones, print '''no'''. No input in this field will show all variants. All following columns in the table show the features in the organisms that are assigned with functional roles. The column headers display the abbreviations of the functional roles (see Functional Roles Table) Hovering over a column header will show a tooltip with the full name of the role. The feature entries in the cells for the functional roles are linked to the [[SEED_Viewer_Manual/Annotation|Annotation Page]] for that feature. There can be multiple features in a cell, as some functions are implemented by more that one feature in an organism. [[Image:SubsystemSpreadsheet.png]] === Description === === Additional Notes === 446bc17af0b02d0129e8615f4d06f12738711345 2117 2116 2008-11-25T16:46:27Z DanielaBartels 10 /* Spreadsheet */ wikitext text/x-wiki == Subsystems == A [[Glossary#Subsystem|subsystem]] is a collection of [[Glossary#Functional role|functional roles]] that are associated to each other in a system. Such a system can be a metabolic pathway, a component if a cell like a secretion system and others. The subsystem page in the SeedViewer is divided into different parts via a [[WebComponent/Tabview|TabView]]. The TabView can consist of 3-5 tabs. The first tab shows a '''Diagram''' of the subsystem, the second tab displays a [[WebComponents/Table|table]] with the '''Functional Roles''' present in the subsystem. The '''Spreadsheet''' showing relating the functional roles in the subsystem to features in genomes can be found in the third tab. The fourth and fifth tab show a description and additional notes to a subsystem. They only appear if a subsystem has a description / notes. === Diagram === The subsystem diagram shows the connections between the functional roles in a subsystem. The boxes represent the functional roles via their abbreviations. The circles are connecting intermediates, that are described in the table which is part of the diagram. The functional roles in the diagram can be colored according to their presence in a genome. Click the button '''Color Diagram''' to get a combo box with all genomes in the subsystem. Select your genome of interest and press '''do coloring'''. The boxes for the functional roles defined for that genome will now be colored in green. [[Image:SubsystemDiagram.png]] === Functional Roles === This [[WebComponents/Table|table]] lists all functional roles present in the subsystem. The first column shows '''Group Aliases''' for the functional role. Functional roles can be aggregated in groups (subsets). Subset names that start with a '*' contain alternative ways to implement a function. The abbreviation ('''Abbrev.''') for a functional role must be unique for the functional roles in the subsystem. They are used in different displays like the Diagram or the Speadsheet. The third column lists the full name of the functional role. EC-Numbers are often part of the functional role (for enzymes), and are stated in parentheses after the name of the functional role. The following two columns deal with reactions a functional role is connected to. Clicking on the link opens a new window showing the KEGG reaction. Next to annotator-curated KEGG reactions, we show the KEGG reactions of the curation effort of the [[SEED_People#Hope College|Hope College]] team that collaborates with the SEED. GeneOntology (GO) links are displayed in the next column. The links point to the GO-number in GeneOntology's Amigo-Tool. The last column can contain literature (PubMed IDs) that describes the functional role in detail. If present, you will find a link to PubMed in this column. [[Image:SubsystemFRs.png]] === Spreadsheet === The subsystem spreadsheet displays the features that are assigned with the functional roles in all organisms that are part of the subsystem. The organisms are displayed in the first column. The links lead to the [[SEED_Viewer_Manual/OrganismPage|Organism Page]]. The column header includes a filter option for the organism, doing an infix search on the organism name. The '''Domain''' (Bacterial, Archaeal or Eukaryote) of the organism is shown in the second column. For each organism in the spreadsheet, a '''Variant Code''' is assigned. Usually, there is more than one way to fulfill a subsystem. Metabolic pathways can have alternatives, or parts of the pathway may be present or absent in an organism. [[[Glossary/Variant Code|Variant Codes]] are assigned to the organism to express this behavior. There are two special Variant Codes: '''0''' and '''-1'''. The Variant Code '''-1''' means that the organism has no active variant in this subsystem, meaning it does not implement the subsystem. '''0''' means that the curator has not yet assigned a variant to the genome. Due to the flow of newly sequenced genomes into the SEED, this variant code may show up sometimes. The next column is used to filter active or not active variants. If you want to see only the active ones (default), print '''yes''' into the filter in the column header. For seeing only the not active ones, print '''no'''. No input in this field will show all variants. All following columns in the table show the features in the organisms that are assigned with functional roles. The column headers display the abbreviations of the functional roles (see Functional Roles Table) Hovering over a column header will show a tooltip with the full name of the role. The feature entries in the cells for the functional roles are linked to the [[SEED_Viewer_Manual/Annotation|Annotation Page]] for that feature. There can be multiple features in a cell, as some functions are implemented by more that one feature in an organism. The control table on top of the spreadsheet table lets you change the display in the table: Functional Roles that belong to a subset starting with a '*', meaning they are alternatives for a function, are collapsed in the spreadsheet by default. If you want to expand the subsets, you can do so by checking '''expanded''' in the '''Subsets''' column. The feature entries in the spreadsheet can be colored according to different metaphors using the second column ('''Coloring''') of the table. By default, the features are colored '''by cluster'''. In this case, it is computed which features are close by on the genomic sequence, meaning they cluster. Each computed cluster gets its own color. These colors only have a meaning per genome, meaning that a yellow cluster in one genome has no connection to a yellow cluster in the next genome. Another way to cluster the features are different kinds of attributes. Check the radio box for '''by attribute''' and choose an attribute in the drop down menu. Press '''update''' to change the display. [[Image:SubsystemSpreadsheet.png]] === Description === === Additional Notes === a68fda5578701701ac97fa67da2fcec2bd74e1d0 2118 2117 2008-11-25T16:49:11Z DanielaBartels 10 /* Description */ wikitext text/x-wiki == Subsystems == A [[Glossary#Subsystem|subsystem]] is a collection of [[Glossary#Functional role|functional roles]] that are associated to each other in a system. Such a system can be a metabolic pathway, a component if a cell like a secretion system and others. The subsystem page in the SeedViewer is divided into different parts via a [[WebComponent/Tabview|TabView]]. The TabView can consist of 3-5 tabs. The first tab shows a '''Diagram''' of the subsystem, the second tab displays a [[WebComponents/Table|table]] with the '''Functional Roles''' present in the subsystem. The '''Spreadsheet''' showing relating the functional roles in the subsystem to features in genomes can be found in the third tab. The fourth and fifth tab show a description and additional notes to a subsystem. They only appear if a subsystem has a description / notes. === Diagram === The subsystem diagram shows the connections between the functional roles in a subsystem. The boxes represent the functional roles via their abbreviations. The circles are connecting intermediates, that are described in the table which is part of the diagram. The functional roles in the diagram can be colored according to their presence in a genome. Click the button '''Color Diagram''' to get a combo box with all genomes in the subsystem. Select your genome of interest and press '''do coloring'''. The boxes for the functional roles defined for that genome will now be colored in green. [[Image:SubsystemDiagram.png]] === Functional Roles === This [[WebComponents/Table|table]] lists all functional roles present in the subsystem. The first column shows '''Group Aliases''' for the functional role. Functional roles can be aggregated in groups (subsets). Subset names that start with a '*' contain alternative ways to implement a function. The abbreviation ('''Abbrev.''') for a functional role must be unique for the functional roles in the subsystem. They are used in different displays like the Diagram or the Speadsheet. The third column lists the full name of the functional role. EC-Numbers are often part of the functional role (for enzymes), and are stated in parentheses after the name of the functional role. The following two columns deal with reactions a functional role is connected to. Clicking on the link opens a new window showing the KEGG reaction. Next to annotator-curated KEGG reactions, we show the KEGG reactions of the curation effort of the [[SEED_People#Hope College|Hope College]] team that collaborates with the SEED. GeneOntology (GO) links are displayed in the next column. The links point to the GO-number in GeneOntology's Amigo-Tool. The last column can contain literature (PubMed IDs) that describes the functional role in detail. If present, you will find a link to PubMed in this column. [[Image:SubsystemFRs.png]] === Spreadsheet === The subsystem spreadsheet displays the features that are assigned with the functional roles in all organisms that are part of the subsystem. The organisms are displayed in the first column. The links lead to the [[SEED_Viewer_Manual/OrganismPage|Organism Page]]. The column header includes a filter option for the organism, doing an infix search on the organism name. The '''Domain''' (Bacterial, Archaeal or Eukaryote) of the organism is shown in the second column. For each organism in the spreadsheet, a '''Variant Code''' is assigned. Usually, there is more than one way to fulfill a subsystem. Metabolic pathways can have alternatives, or parts of the pathway may be present or absent in an organism. [[[Glossary/Variant Code|Variant Codes]] are assigned to the organism to express this behavior. There are two special Variant Codes: '''0''' and '''-1'''. The Variant Code '''-1''' means that the organism has no active variant in this subsystem, meaning it does not implement the subsystem. '''0''' means that the curator has not yet assigned a variant to the genome. Due to the flow of newly sequenced genomes into the SEED, this variant code may show up sometimes. The next column is used to filter active or not active variants. If you want to see only the active ones (default), print '''yes''' into the filter in the column header. For seeing only the not active ones, print '''no'''. No input in this field will show all variants. All following columns in the table show the features in the organisms that are assigned with functional roles. The column headers display the abbreviations of the functional roles (see Functional Roles Table) Hovering over a column header will show a tooltip with the full name of the role. The feature entries in the cells for the functional roles are linked to the [[SEED_Viewer_Manual/Annotation|Annotation Page]] for that feature. There can be multiple features in a cell, as some functions are implemented by more that one feature in an organism. The control table on top of the spreadsheet table lets you change the display in the table: Functional Roles that belong to a subset starting with a '*', meaning they are alternatives for a function, are collapsed in the spreadsheet by default. If you want to expand the subsets, you can do so by checking '''expanded''' in the '''Subsets''' column. The feature entries in the spreadsheet can be colored according to different metaphors using the second column ('''Coloring''') of the table. By default, the features are colored '''by cluster'''. In this case, it is computed which features are close by on the genomic sequence, meaning they cluster. Each computed cluster gets its own color. These colors only have a meaning per genome, meaning that a yellow cluster in one genome has no connection to a yellow cluster in the next genome. Another way to cluster the features are different kinds of attributes. Check the radio box for '''by attribute''' and choose an attribute in the drop down menu. Press '''update''' to change the display. [[Image:SubsystemSpreadsheet.png]] === Description === The description of a subsystem gives an overview of the functional roles and their connections in the subsystem. It can give some background information about the system, what organisms it is usually found in and other facts that are of interest. === Additional Notes === 42db715ea2d36c13d9d2554cb1c91c6ed145e799 2119 2118 2008-11-25T16:51:24Z DanielaBartels 10 /* Additional Notes */ wikitext text/x-wiki == Subsystems == A [[Glossary#Subsystem|subsystem]] is a collection of [[Glossary#Functional role|functional roles]] that are associated to each other in a system. Such a system can be a metabolic pathway, a component if a cell like a secretion system and others. The subsystem page in the SeedViewer is divided into different parts via a [[WebComponent/Tabview|TabView]]. The TabView can consist of 3-5 tabs. The first tab shows a '''Diagram''' of the subsystem, the second tab displays a [[WebComponents/Table|table]] with the '''Functional Roles''' present in the subsystem. The '''Spreadsheet''' showing relating the functional roles in the subsystem to features in genomes can be found in the third tab. The fourth and fifth tab show a description and additional notes to a subsystem. They only appear if a subsystem has a description / notes. === Diagram === The subsystem diagram shows the connections between the functional roles in a subsystem. The boxes represent the functional roles via their abbreviations. The circles are connecting intermediates, that are described in the table which is part of the diagram. The functional roles in the diagram can be colored according to their presence in a genome. Click the button '''Color Diagram''' to get a combo box with all genomes in the subsystem. Select your genome of interest and press '''do coloring'''. The boxes for the functional roles defined for that genome will now be colored in green. [[Image:SubsystemDiagram.png]] === Functional Roles === This [[WebComponents/Table|table]] lists all functional roles present in the subsystem. The first column shows '''Group Aliases''' for the functional role. Functional roles can be aggregated in groups (subsets). Subset names that start with a '*' contain alternative ways to implement a function. The abbreviation ('''Abbrev.''') for a functional role must be unique for the functional roles in the subsystem. They are used in different displays like the Diagram or the Speadsheet. The third column lists the full name of the functional role. EC-Numbers are often part of the functional role (for enzymes), and are stated in parentheses after the name of the functional role. The following two columns deal with reactions a functional role is connected to. Clicking on the link opens a new window showing the KEGG reaction. Next to annotator-curated KEGG reactions, we show the KEGG reactions of the curation effort of the [[SEED_People#Hope College|Hope College]] team that collaborates with the SEED. GeneOntology (GO) links are displayed in the next column. The links point to the GO-number in GeneOntology's Amigo-Tool. The last column can contain literature (PubMed IDs) that describes the functional role in detail. If present, you will find a link to PubMed in this column. [[Image:SubsystemFRs.png]] === Spreadsheet === The subsystem spreadsheet displays the features that are assigned with the functional roles in all organisms that are part of the subsystem. The organisms are displayed in the first column. The links lead to the [[SEED_Viewer_Manual/OrganismPage|Organism Page]]. The column header includes a filter option for the organism, doing an infix search on the organism name. The '''Domain''' (Bacterial, Archaeal or Eukaryote) of the organism is shown in the second column. For each organism in the spreadsheet, a '''Variant Code''' is assigned. Usually, there is more than one way to fulfill a subsystem. Metabolic pathways can have alternatives, or parts of the pathway may be present or absent in an organism. [[[Glossary/Variant Code|Variant Codes]] are assigned to the organism to express this behavior. There are two special Variant Codes: '''0''' and '''-1'''. The Variant Code '''-1''' means that the organism has no active variant in this subsystem, meaning it does not implement the subsystem. '''0''' means that the curator has not yet assigned a variant to the genome. Due to the flow of newly sequenced genomes into the SEED, this variant code may show up sometimes. The next column is used to filter active or not active variants. If you want to see only the active ones (default), print '''yes''' into the filter in the column header. For seeing only the not active ones, print '''no'''. No input in this field will show all variants. All following columns in the table show the features in the organisms that are assigned with functional roles. The column headers display the abbreviations of the functional roles (see Functional Roles Table) Hovering over a column header will show a tooltip with the full name of the role. The feature entries in the cells for the functional roles are linked to the [[SEED_Viewer_Manual/Annotation|Annotation Page]] for that feature. There can be multiple features in a cell, as some functions are implemented by more that one feature in an organism. The control table on top of the spreadsheet table lets you change the display in the table: Functional Roles that belong to a subset starting with a '*', meaning they are alternatives for a function, are collapsed in the spreadsheet by default. If you want to expand the subsets, you can do so by checking '''expanded''' in the '''Subsets''' column. The feature entries in the spreadsheet can be colored according to different metaphors using the second column ('''Coloring''') of the table. By default, the features are colored '''by cluster'''. In this case, it is computed which features are close by on the genomic sequence, meaning they cluster. Each computed cluster gets its own color. These colors only have a meaning per genome, meaning that a yellow cluster in one genome has no connection to a yellow cluster in the next genome. Another way to cluster the features are different kinds of attributes. Check the radio box for '''by attribute''' and choose an attribute in the drop down menu. Press '''update''' to change the display. [[Image:SubsystemSpreadsheet.png]] === Description === The description of a subsystem gives an overview of the functional roles and their connections in the subsystem. It can give some background information about the system, what organisms it is usually found in and other facts that are of interest. === Additional Notes === As the description already gives an overview over the subsystem, additional notes can be found here. The notes usually refer to specific properties of some organisms or organism groups, genes that are missing but should be there and other details that might be usefull for the interested user. e4d342492ad0aa7f2503e2e4ef03bba938090ff5 2120 2119 2008-11-25T16:52:34Z DanielaBartels 10 /* Additional Notes */ wikitext text/x-wiki == Subsystems == A [[Glossary#Subsystem|subsystem]] is a collection of [[Glossary#Functional role|functional roles]] that are associated to each other in a system. Such a system can be a metabolic pathway, a component if a cell like a secretion system and others. The subsystem page in the SeedViewer is divided into different parts via a [[WebComponent/Tabview|TabView]]. The TabView can consist of 3-5 tabs. The first tab shows a '''Diagram''' of the subsystem, the second tab displays a [[WebComponents/Table|table]] with the '''Functional Roles''' present in the subsystem. The '''Spreadsheet''' showing relating the functional roles in the subsystem to features in genomes can be found in the third tab. The fourth and fifth tab show a description and additional notes to a subsystem. They only appear if a subsystem has a description / notes. === Diagram === The subsystem diagram shows the connections between the functional roles in a subsystem. The boxes represent the functional roles via their abbreviations. The circles are connecting intermediates, that are described in the table which is part of the diagram. The functional roles in the diagram can be colored according to their presence in a genome. Click the button '''Color Diagram''' to get a combo box with all genomes in the subsystem. Select your genome of interest and press '''do coloring'''. The boxes for the functional roles defined for that genome will now be colored in green. [[Image:SubsystemDiagram.png]] === Functional Roles === This [[WebComponents/Table|table]] lists all functional roles present in the subsystem. The first column shows '''Group Aliases''' for the functional role. Functional roles can be aggregated in groups (subsets). Subset names that start with a '*' contain alternative ways to implement a function. The abbreviation ('''Abbrev.''') for a functional role must be unique for the functional roles in the subsystem. They are used in different displays like the Diagram or the Speadsheet. The third column lists the full name of the functional role. EC-Numbers are often part of the functional role (for enzymes), and are stated in parentheses after the name of the functional role. The following two columns deal with reactions a functional role is connected to. Clicking on the link opens a new window showing the KEGG reaction. Next to annotator-curated KEGG reactions, we show the KEGG reactions of the curation effort of the [[SEED_People#Hope College|Hope College]] team that collaborates with the SEED. GeneOntology (GO) links are displayed in the next column. The links point to the GO-number in GeneOntology's Amigo-Tool. The last column can contain literature (PubMed IDs) that describes the functional role in detail. If present, you will find a link to PubMed in this column. [[Image:SubsystemFRs.png]] === Spreadsheet === The subsystem spreadsheet displays the features that are assigned with the functional roles in all organisms that are part of the subsystem. The organisms are displayed in the first column. The links lead to the [[SEED_Viewer_Manual/OrganismPage|Organism Page]]. The column header includes a filter option for the organism, doing an infix search on the organism name. The '''Domain''' (Bacterial, Archaeal or Eukaryote) of the organism is shown in the second column. For each organism in the spreadsheet, a '''Variant Code''' is assigned. Usually, there is more than one way to fulfill a subsystem. Metabolic pathways can have alternatives, or parts of the pathway may be present or absent in an organism. [[[Glossary/Variant Code|Variant Codes]] are assigned to the organism to express this behavior. There are two special Variant Codes: '''0''' and '''-1'''. The Variant Code '''-1''' means that the organism has no active variant in this subsystem, meaning it does not implement the subsystem. '''0''' means that the curator has not yet assigned a variant to the genome. Due to the flow of newly sequenced genomes into the SEED, this variant code may show up sometimes. The next column is used to filter active or not active variants. If you want to see only the active ones (default), print '''yes''' into the filter in the column header. For seeing only the not active ones, print '''no'''. No input in this field will show all variants. All following columns in the table show the features in the organisms that are assigned with functional roles. The column headers display the abbreviations of the functional roles (see Functional Roles Table) Hovering over a column header will show a tooltip with the full name of the role. The feature entries in the cells for the functional roles are linked to the [[SEED_Viewer_Manual/Annotation|Annotation Page]] for that feature. There can be multiple features in a cell, as some functions are implemented by more that one feature in an organism. The control table on top of the spreadsheet table lets you change the display in the table: Functional Roles that belong to a subset starting with a '*', meaning they are alternatives for a function, are collapsed in the spreadsheet by default. If you want to expand the subsets, you can do so by checking '''expanded''' in the '''Subsets''' column. The feature entries in the spreadsheet can be colored according to different metaphors using the second column ('''Coloring''') of the table. By default, the features are colored '''by cluster'''. In this case, it is computed which features are close by on the genomic sequence, meaning they cluster. Each computed cluster gets its own color. These colors only have a meaning per genome, meaning that a yellow cluster in one genome has no connection to a yellow cluster in the next genome. Another way to cluster the features are different kinds of attributes. Check the radio box for '''by attribute''' and choose an attribute in the drop down menu. Press '''update''' to change the display. [[Image:SubsystemSpreadsheet.png]] === Description === The description of a subsystem gives an overview of the functional roles and their connections in the subsystem. It can give some background information about the system, what organisms it is usually found in and other facts that are of interest. === Additional Notes === As the description already gives an overview over the subsystem, additional notes can be found here. The notes usually refer to specific properties of some organisms or organism groups, genes that are missing but should be there and other details that might be useful for the interested user. 3cdb0c78b0c8eed76bbc363fc892e9bae40fe225 2122 2120 2008-11-25T16:56:22Z TobiasPaczian 17 /* Subsystems */ wikitext text/x-wiki == Subsystems == A [[Glossary#Subsystem|subsystem]] is a collection of [[Glossary#Functional role|functional roles]] that are associated to each other in a system. Such a system can be a metabolic pathway, a component of a cell like a secretion system and others. The subsystem page in the SeedViewer is divided into different parts via a [[WebComponent/Tabview|TabView]]. The TabView can consist of 3-5 tabs. The first tab shows a '''Diagram''' of the subsystem, the second tab displays a [[WebComponents/Table|table]] with the '''Functional Roles''' present in the subsystem. The '''Spreadsheet''' showing relating the functional roles in the subsystem to features in genomes can be found in the third tab. The fourth and fifth tab show a description and additional notes to a subsystem. They only appear if a subsystem has a description / notes. === Diagram === The subsystem diagram shows the connections between the functional roles in a subsystem. The boxes represent the functional roles via their abbreviations. The circles are connecting intermediates, that are described in the table which is part of the diagram. The functional roles in the diagram can be colored according to their presence in a genome. Click the button '''Color Diagram''' to get a combo box with all genomes in the subsystem. Select your genome of interest and press '''do coloring'''. The boxes for the functional roles defined for that genome will now be colored in green. [[Image:SubsystemDiagram.png]] === Functional Roles === This [[WebComponents/Table|table]] lists all functional roles present in the subsystem. The first column shows '''Group Aliases''' for the functional role. Functional roles can be aggregated in groups (subsets). Subset names that start with a '*' contain alternative ways to implement a function. The abbreviation ('''Abbrev.''') for a functional role must be unique for the functional roles in the subsystem. They are used in different displays like the Diagram or the Speadsheet. The third column lists the full name of the functional role. EC-Numbers are often part of the functional role (for enzymes), and are stated in parentheses after the name of the functional role. The following two columns deal with reactions a functional role is connected to. Clicking on the link opens a new window showing the KEGG reaction. Next to annotator-curated KEGG reactions, we show the KEGG reactions of the curation effort of the [[SEED_People#Hope College|Hope College]] team that collaborates with the SEED. GeneOntology (GO) links are displayed in the next column. The links point to the GO-number in GeneOntology's Amigo-Tool. The last column can contain literature (PubMed IDs) that describes the functional role in detail. If present, you will find a link to PubMed in this column. [[Image:SubsystemFRs.png]] === Spreadsheet === The subsystem spreadsheet displays the features that are assigned with the functional roles in all organisms that are part of the subsystem. The organisms are displayed in the first column. The links lead to the [[SEED_Viewer_Manual/OrganismPage|Organism Page]]. The column header includes a filter option for the organism, doing an infix search on the organism name. The '''Domain''' (Bacterial, Archaeal or Eukaryote) of the organism is shown in the second column. For each organism in the spreadsheet, a '''Variant Code''' is assigned. Usually, there is more than one way to fulfill a subsystem. Metabolic pathways can have alternatives, or parts of the pathway may be present or absent in an organism. [[[Glossary/Variant Code|Variant Codes]] are assigned to the organism to express this behavior. There are two special Variant Codes: '''0''' and '''-1'''. The Variant Code '''-1''' means that the organism has no active variant in this subsystem, meaning it does not implement the subsystem. '''0''' means that the curator has not yet assigned a variant to the genome. Due to the flow of newly sequenced genomes into the SEED, this variant code may show up sometimes. The next column is used to filter active or not active variants. If you want to see only the active ones (default), print '''yes''' into the filter in the column header. For seeing only the not active ones, print '''no'''. No input in this field will show all variants. All following columns in the table show the features in the organisms that are assigned with functional roles. The column headers display the abbreviations of the functional roles (see Functional Roles Table) Hovering over a column header will show a tooltip with the full name of the role. The feature entries in the cells for the functional roles are linked to the [[SEED_Viewer_Manual/Annotation|Annotation Page]] for that feature. There can be multiple features in a cell, as some functions are implemented by more that one feature in an organism. The control table on top of the spreadsheet table lets you change the display in the table: Functional Roles that belong to a subset starting with a '*', meaning they are alternatives for a function, are collapsed in the spreadsheet by default. If you want to expand the subsets, you can do so by checking '''expanded''' in the '''Subsets''' column. The feature entries in the spreadsheet can be colored according to different metaphors using the second column ('''Coloring''') of the table. By default, the features are colored '''by cluster'''. In this case, it is computed which features are close by on the genomic sequence, meaning they cluster. Each computed cluster gets its own color. These colors only have a meaning per genome, meaning that a yellow cluster in one genome has no connection to a yellow cluster in the next genome. Another way to cluster the features are different kinds of attributes. Check the radio box for '''by attribute''' and choose an attribute in the drop down menu. Press '''update''' to change the display. [[Image:SubsystemSpreadsheet.png]] === Description === The description of a subsystem gives an overview of the functional roles and their connections in the subsystem. It can give some background information about the system, what organisms it is usually found in and other facts that are of interest. === Additional Notes === As the description already gives an overview over the subsystem, additional notes can be found here. The notes usually refer to specific properties of some organisms or organism groups, genes that are missing but should be there and other details that might be useful for the interested user. 8deffe0170dfff1dbd48e8f385cbdd2eaad292f6 2127 2122 2008-11-26T09:01:53Z DanielaBartels 10 /* Subsystems */ wikitext text/x-wiki == Subsystems == A [[Glossary#Subsystem|subsystem]] is a collection of [[Glossary#Functional role|functional roles]] that are associated to each other in a system. Such a system can be a metabolic pathway, a component of a cell like a secretion system and others. The subsystem page in the SeedViewer is divided into different parts via a [[WebComponents/Tabview|TabView]]. The TabView can consist of 3-5 tabs. The first tab shows a '''Diagram''' of the subsystem, the second tab displays a [[WebComponents/Table|table]] with the '''Functional Roles''' present in the subsystem. The '''Spreadsheet''' showing relating the functional roles in the subsystem to features in genomes can be found in the third tab. The fourth and fifth tab show a description and additional notes to a subsystem. They only appear if a subsystem has a description / notes. === Diagram === The subsystem diagram shows the connections between the functional roles in a subsystem. The boxes represent the functional roles via their abbreviations. The circles are connecting intermediates, that are described in the table which is part of the diagram. The functional roles in the diagram can be colored according to their presence in a genome. Click the button '''Color Diagram''' to get a combo box with all genomes in the subsystem. Select your genome of interest and press '''do coloring'''. The boxes for the functional roles defined for that genome will now be colored in green. [[Image:SubsystemDiagram.png]] === Functional Roles === This [[WebComponents/Table|table]] lists all functional roles present in the subsystem. The first column shows '''Group Aliases''' for the functional role. Functional roles can be aggregated in groups (subsets). Subset names that start with a '*' contain alternative ways to implement a function. The abbreviation ('''Abbrev.''') for a functional role must be unique for the functional roles in the subsystem. They are used in different displays like the Diagram or the Speadsheet. The third column lists the full name of the functional role. EC-Numbers are often part of the functional role (for enzymes), and are stated in parentheses after the name of the functional role. The following two columns deal with reactions a functional role is connected to. Clicking on the link opens a new window showing the KEGG reaction. Next to annotator-curated KEGG reactions, we show the KEGG reactions of the curation effort of the [[SEED_People#Hope College|Hope College]] team that collaborates with the SEED. GeneOntology (GO) links are displayed in the next column. The links point to the GO-number in GeneOntology's Amigo-Tool. The last column can contain literature (PubMed IDs) that describes the functional role in detail. If present, you will find a link to PubMed in this column. [[Image:SubsystemFRs.png]] === Spreadsheet === The subsystem spreadsheet displays the features that are assigned with the functional roles in all organisms that are part of the subsystem. The organisms are displayed in the first column. The links lead to the [[SEED_Viewer_Manual/OrganismPage|Organism Page]]. The column header includes a filter option for the organism, doing an infix search on the organism name. The '''Domain''' (Bacterial, Archaeal or Eukaryote) of the organism is shown in the second column. For each organism in the spreadsheet, a '''Variant Code''' is assigned. Usually, there is more than one way to fulfill a subsystem. Metabolic pathways can have alternatives, or parts of the pathway may be present or absent in an organism. [[[Glossary/Variant Code|Variant Codes]] are assigned to the organism to express this behavior. There are two special Variant Codes: '''0''' and '''-1'''. The Variant Code '''-1''' means that the organism has no active variant in this subsystem, meaning it does not implement the subsystem. '''0''' means that the curator has not yet assigned a variant to the genome. Due to the flow of newly sequenced genomes into the SEED, this variant code may show up sometimes. The next column is used to filter active or not active variants. If you want to see only the active ones (default), print '''yes''' into the filter in the column header. For seeing only the not active ones, print '''no'''. No input in this field will show all variants. All following columns in the table show the features in the organisms that are assigned with functional roles. The column headers display the abbreviations of the functional roles (see Functional Roles Table) Hovering over a column header will show a tooltip with the full name of the role. The feature entries in the cells for the functional roles are linked to the [[SEED_Viewer_Manual/Annotation|Annotation Page]] for that feature. There can be multiple features in a cell, as some functions are implemented by more that one feature in an organism. The control table on top of the spreadsheet table lets you change the display in the table: Functional Roles that belong to a subset starting with a '*', meaning they are alternatives for a function, are collapsed in the spreadsheet by default. If you want to expand the subsets, you can do so by checking '''expanded''' in the '''Subsets''' column. The feature entries in the spreadsheet can be colored according to different metaphors using the second column ('''Coloring''') of the table. By default, the features are colored '''by cluster'''. In this case, it is computed which features are close by on the genomic sequence, meaning they cluster. Each computed cluster gets its own color. These colors only have a meaning per genome, meaning that a yellow cluster in one genome has no connection to a yellow cluster in the next genome. Another way to cluster the features are different kinds of attributes. Check the radio box for '''by attribute''' and choose an attribute in the drop down menu. Press '''update''' to change the display. [[Image:SubsystemSpreadsheet.png]] === Description === The description of a subsystem gives an overview of the functional roles and their connections in the subsystem. It can give some background information about the system, what organisms it is usually found in and other facts that are of interest. === Additional Notes === As the description already gives an overview over the subsystem, additional notes can be found here. The notes usually refer to specific properties of some organisms or organism groups, genes that are missing but should be there and other details that might be useful for the interested user. b685e862028a8b5eb320c4559633fcddee3cbefd 6 1518 2102 2008-11-25T14:23:56Z DanielaBartels 10 wikitext text/x-wiki da39a3ee5e6b4b0d3255bfef95601890afd80709 6 1519 2103 2008-11-25T14:32:00Z DanielaBartels 10 wikitext text/x-wiki da39a3ee5e6b4b0d3255bfef95601890afd80709 6 1520 2104 2008-11-25T14:33:26Z DanielaBartels 10 wikitext text/x-wiki da39a3ee5e6b4b0d3255bfef95601890afd80709 6 1521 2106 2008-11-25T14:34:39Z DanielaBartels 10 wikitext text/x-wiki da39a3ee5e6b4b0d3255bfef95601890afd80709 0 1466 2121 2037 2008-11-25T16:53:58Z DanielaBartels 10 /* Main pages of the SeedViewer */ wikitext text/x-wiki == Main pages of the SeedViewer == ''' [[SEED_Viewer_Manual|Home Page]] ''' ''' [[SEED_Viewer_Manual/Menu|Menu]] ''' === Subsystem Select === '''[[SEED_Viewer_Manual/Subsystems|Subsystems]]''' === Functional Role === === FigFams === '''[[SEED_Viewer_Manual/Annotation|Annotation]]''' '''[[SEED_Viewer_Manual/Evidence|Evidence]]''' '''[[SEED_Viewer_Manual/BLASTOrganism|BLAST against an organism]]''' === Sequence === '''[[SEED_Viewer_Manual/GenomeBrowser|Browse Genome]]''' '''[[SEED_Viewer_Manual/OrganismSelect|Organism Select]]''' '''[[SEED_Viewer_Manual/OrganismPage|Organism Page]]''' === Kegg === '''[[SEED_Viewer_Manual/HomologClusters|Homolog Clusters]]''' ae5cd4ef52e82459fac878fec043924cd2b8aa33 6 1523 2124 2008-11-26T08:55:25Z DanielaBartels 10 wikitext text/x-wiki da39a3ee5e6b4b0d3255bfef95601890afd80709 0 1524 2125 2008-11-26T08:58:41Z DanielaBartels 10 wikitext text/x-wiki == The TabView == The TabView component is used on many pages in the [[SEED_Viewer_Manual|SeedViewer]]. It is useful at places where you have different options to access data or you need to fulfill a task step-by-step. The entire content of the TabView is loaded when you enter the page. Clicking a different tab only displays the data which was hidden before. At the top of the TabView, you can access the different tabs. In the example (SeedViewer Mainpage), the chosen tab is white, while all hidden tabs have a green header. Click on the green header will activate the respective tab. [[Image:TabView.png]] 0a3af82736a3504de9a46ee89a57cca0a609c542 0 1525 2128 2008-11-26T09:15:48Z DanielaBartels 10 wikitext text/x-wiki == Table == The Table component has a large number of functionalities that can be used to access data that can be displayed in tabular form. Features of the table component are '''Browsing''', '''Sorting''', '''Filtering''' and '''Export'''. === Browsing === === Sorting === === Filtering === === Export === e4d7bb5fe130809f5f782378dd8f8331a852d137 2129 2128 2008-11-26T09:27:59Z DanielaBartels 10 /* Table */ wikitext text/x-wiki == Table == The Table component has a large number of functionalities that can be used to access data that can be displayed in tabular form. Features of the table component are '''Browsing''', '''Sorting''', '''Filtering''' and '''Export'''. === Browsing === [[Image::TableBrowse.png]] === Sorting === [[Image::TableSort.png]] === Filtering === [[Image::TableFilter1.png]] [[Image::TableFilter2.png]] [[Image::TableFilter3.png]] === Export === 2de19cf6d2a39ef70c25273895e980cd61a06dd6 6 1526 2130 2008-11-26T09:28:21Z DanielaBartels 10 wikitext text/x-wiki da39a3ee5e6b4b0d3255bfef95601890afd80709 0 1525 2131 2129 2008-11-26T09:28:44Z DanielaBartels 10 /* Table */ wikitext text/x-wiki == Table == The Table component has a large number of functionalities that can be used to access data that can be displayed in tabular form. Features of the table component are '''Browsing''', '''Sorting''', '''Filtering''' and '''Export'''. === Browsing === [[Image:TableBrowse.png]] === Sorting === [[Image:TableSort.png]] === Filtering === [[Image:TableFilter1.png]] [[Image:TableFilter2.png]] [[Image:TableFilter3.png]] === Export === 6c9d02b75389010a4c209bf16f8ac66162a9eb63 2134 2131 2008-11-26T09:39:01Z DanielaBartels 10 /* Table */ wikitext text/x-wiki == Table == The Table component has a large number of functionalities that can be used to access data that can be displayed in tabular form. Features of the table component are '''Browsing''', '''Sorting''', '''Filtering''' and '''Export'''. [[Image:Table1.png]] === Browsing === [[Image:TableBrowse.png]] === Sorting === [[Image:TableSort.png]] === Filtering === [[Image:TableFilter1.png]] [[Image:TableFilter2.png]] [[Image:TableFilter3.png]] === Export === 5f279737695c6e1e14727c5b85d959277d4e8e33 2137 2134 2008-11-26T09:52:11Z DanielaBartels 10 /* Table */ wikitext text/x-wiki == Table == The Table component has a large number of functionalities that can be used to access data that can be displayed in tabular form. Features of the table component are '''Browsing''', '''Sorting''', '''Filtering''' and '''Export'''. A table consists of a header row (here in dark blue) and the rows that contain the data. [[Image:Table1.png]] === Browsing === [[Image:TableBrowse.png]] === Sorting === [[Image:TableSort.png]] === Filtering === [[Image:TableFilter1.png]] [[Image:TableFilter2.png]] [[Image:TableFilter3.png]] === Export === 6e089f580480e04f033aaf3f5c05743e1b081462 2138 2137 2008-11-26T09:58:11Z DanielaBartels 10 /* Table */ wikitext text/x-wiki == Table == The Table component has a large number of functionalities that can be used to access data that can be displayed in tabular form. Features of the table component are '''Browsing''', '''Sorting''', '''Filtering''' and '''Export'''. A table consists of a header row (here in dark blue) and the rows that contain the data. In some cases the header row can be supplied with a supercolumn to group columns. The header cells contain the functionality to sort and filter the row data, as described below. The rows are colored in two different colors for better visibility (here white and light grey background). If you hover over a row, it will be highlighted in dark grey. [[Image:Table1.png]] === Browsing === [[Image:TableBrowse.png]] === Sorting === [[Image:TableSort.png]] === Filtering === [[Image:TableFilter1.png]] [[Image:TableFilter2.png]] [[Image:TableFilter3.png]] === Export === decc37450b255bb31cd90df8448a58d0ae06c347 2139 2138 2008-11-26T10:31:42Z DanielaBartels 10 /* Browsing */ wikitext text/x-wiki == Table == The Table component has a large number of functionalities that can be used to access data that can be displayed in tabular form. Features of the table component are '''Browsing''', '''Sorting''', '''Filtering''' and '''Export'''. A table consists of a header row (here in dark blue) and the rows that contain the data. In some cases the header row can be supplied with a supercolumn to group columns. The header cells contain the functionality to sort and filter the row data, as described below. The rows are colored in two different colors for better visibility (here white and light grey background). If you hover over a row, it will be highlighted in dark grey. [[Image:Table1.png]] === Browsing === The number of rows you want your table to display at once can be changed using the text box '''display ___ items per page'''. [[Image:TableBrowse.png]] === Sorting === [[Image:TableSort.png]] === Filtering === [[Image:TableFilter1.png]] [[Image:TableFilter2.png]] [[Image:TableFilter3.png]] === Export === 1293149c9fba4d18d9499ee783d1e118f3588845 2140 2139 2008-11-26T10:34:40Z DanielaBartels 10 /* Browsing */ wikitext text/x-wiki == Table == The Table component has a large number of functionalities that can be used to access data that can be displayed in tabular form. Features of the table component are '''Browsing''', '''Sorting''', '''Filtering''' and '''Export'''. A table consists of a header row (here in dark blue) and the rows that contain the data. In some cases the header row can be supplied with a supercolumn to group columns. The header cells contain the functionality to sort and filter the row data, as described below. The rows are colored in two different colors for better visibility (here white and light grey background). If you hover over a row, it will be highlighted in dark grey. [[Image:Table1.png]] === Browsing === The number of rows you want your table to display at once can be changed using the text box '''display ___ items per page'''. Just press return after changing the number to change the display of your table. To browse through the table you can click the links '''<<first''', '''<<prev''', '''next>>''' and '''last>>'''. The links only appear if there is e.g. a next page. [[Image:TableBrowse.png]] === Sorting === [[Image:TableSort.png]] === Filtering === [[Image:TableFilter1.png]] [[Image:TableFilter2.png]] [[Image:TableFilter3.png]] === Export === a1187b069d8f90fbc121274832e22a5ed52b3f83 2141 2140 2008-11-26T10:35:18Z DanielaBartels 10 /* Browsing */ wikitext text/x-wiki == Table == The Table component has a large number of functionalities that can be used to access data that can be displayed in tabular form. Features of the table component are '''Browsing''', '''Sorting''', '''Filtering''' and '''Export'''. A table consists of a header row (here in dark blue) and the rows that contain the data. In some cases the header row can be supplied with a supercolumn to group columns. The header cells contain the functionality to sort and filter the row data, as described below. The rows are colored in two different colors for better visibility (here white and light grey background). If you hover over a row, it will be highlighted in dark grey. [[Image:Table1.png]] === Browsing === The number of rows you want your table to display at once can be changed using the text box '''display ___ items per page'''. Just press return after changing the number to change the display of your table. To browse through the table you can click the links '''<<first''', '''<<prev''', '''next>>''' and '''last>>'''. The links only appear if there is e.g. a next page. The text in the middle of the links will tell you which items are currently displayed. [[Image:TableBrowse.png]] === Sorting === [[Image:TableSort.png]] === Filtering === [[Image:TableFilter1.png]] [[Image:TableFilter2.png]] [[Image:TableFilter3.png]] === Export === f06caefa61f7ae73ef80d98bf1a42b72150fcae0 2143 2141 2008-11-26T10:39:04Z DanielaBartels 10 /* Sorting */ wikitext text/x-wiki == Table == The Table component has a large number of functionalities that can be used to access data that can be displayed in tabular form. Features of the table component are '''Browsing''', '''Sorting''', '''Filtering''' and '''Export'''. A table consists of a header row (here in dark blue) and the rows that contain the data. In some cases the header row can be supplied with a supercolumn to group columns. The header cells contain the functionality to sort and filter the row data, as described below. The rows are colored in two different colors for better visibility (here white and light grey background). If you hover over a row, it will be highlighted in dark grey. [[Image:Table1.png]] === Browsing === The number of rows you want your table to display at once can be changed using the text box '''display ___ items per page'''. Just press return after changing the number to change the display of your table. To browse through the table you can click the links '''<<first''', '''<<prev''', '''next>>''' and '''last>>'''. The links only appear if there is e.g. a next page. The text in the middle of the links will tell you which items are currently displayed. [[Image:TableBrowse.png]] === Sorting === You can sort the contents of the table by each column using the little arrows next to the column header. The sorting is done using JavaScript, meaning that it does not reload the page. [[Image:TableSort.png]] === Filtering === [[Image:TableFilter1.png]] [[Image:TableFilter2.png]] [[Image:TableFilter3.png]] === Export === 450ea46a23af63dc01aabe1b630ed0dcef8378a7 2144 2143 2008-11-26T10:40:49Z DanielaBartels 10 /* Table */ wikitext text/x-wiki == Table == The Table component has a large number of functionalities that can be used to access data that can be displayed in tabular form. Features of the table component are '''Browsing''', '''Sorting''', '''Filtering''' and '''Export'''. Most of these functions of the table are implemented by JavaScript functions. That means, it does not lead to a reload of the page. The page ''knows'' all the information, but only part of it is displayed. The display is then manipulated using JavaScript functions. A table consists of a header row (here in dark blue) and the rows that contain the data. In some cases the header row can be supplied with a supercolumn to group columns. The header cells contain the functionality to sort and filter the row data, as described below. The rows are colored in two different colors for better visibility (here white and light grey background). If you hover over a row, it will be highlighted in dark grey. [[Image:Table1.png]] === Browsing === The number of rows you want your table to display at once can be changed using the text box '''display ___ items per page'''. Just press return after changing the number to change the display of your table. To browse through the table you can click the links '''<<first''', '''<<prev''', '''next>>''' and '''last>>'''. The links only appear if there is e.g. a next page. The text in the middle of the links will tell you which items are currently displayed. [[Image:TableBrowse.png]] === Sorting === You can sort the contents of the table by each column using the little arrows next to the column header. The sorting is done using JavaScript, meaning that it does not reload the page. [[Image:TableSort.png]] === Filtering === [[Image:TableFilter1.png]] [[Image:TableFilter2.png]] [[Image:TableFilter3.png]] === Export === a53c1527d3ddbce9fee6bb35cb6b67f56b57e730 2145 2144 2008-11-26T10:43:22Z DanielaBartels 10 /* Filtering */ wikitext text/x-wiki == Table == The Table component has a large number of functionalities that can be used to access data that can be displayed in tabular form. Features of the table component are '''Browsing''', '''Sorting''', '''Filtering''' and '''Export'''. Most of these functions of the table are implemented by JavaScript functions. That means, it does not lead to a reload of the page. The page ''knows'' all the information, but only part of it is displayed. The display is then manipulated using JavaScript functions. A table consists of a header row (here in dark blue) and the rows that contain the data. In some cases the header row can be supplied with a supercolumn to group columns. The header cells contain the functionality to sort and filter the row data, as described below. The rows are colored in two different colors for better visibility (here white and light grey background). If you hover over a row, it will be highlighted in dark grey. [[Image:Table1.png]] === Browsing === The number of rows you want your table to display at once can be changed using the text box '''display ___ items per page'''. Just press return after changing the number to change the display of your table. To browse through the table you can click the links '''<<first''', '''<<prev''', '''next>>''' and '''last>>'''. The links only appear if there is e.g. a next page. The text in the middle of the links will tell you which items are currently displayed. [[Image:TableBrowse.png]] === Sorting === You can sort the contents of the table by each column using the little arrows next to the column header. The sorting is done using JavaScript, meaning that it does not reload the page. [[Image:TableSort.png]] === Filtering === Different kinds of filters can be applied to the table data. One filter is simply a text field that does an infix search (meaning that if the word you type in the text field is part of a word in the cells of a cell in the respective column, the row will be visible. [[Image:TableFilter1.png]] [[Image:TableFilter2.png]] [[Image:TableFilter3.png]] === Export === e45034309de8a83beac1931914a604c773bf7e25 2146 2145 2008-11-26T11:03:42Z DanielaBartels 10 /* Filtering */ wikitext text/x-wiki == Table == The Table component has a large number of functionalities that can be used to access data that can be displayed in tabular form. Features of the table component are '''Browsing''', '''Sorting''', '''Filtering''' and '''Export'''. Most of these functions of the table are implemented by JavaScript functions. That means, it does not lead to a reload of the page. The page ''knows'' all the information, but only part of it is displayed. The display is then manipulated using JavaScript functions. A table consists of a header row (here in dark blue) and the rows that contain the data. In some cases the header row can be supplied with a supercolumn to group columns. The header cells contain the functionality to sort and filter the row data, as described below. The rows are colored in two different colors for better visibility (here white and light grey background). If you hover over a row, it will be highlighted in dark grey. [[Image:Table1.png]] === Browsing === The number of rows you want your table to display at once can be changed using the text box '''display ___ items per page'''. Just press return after changing the number to change the display of your table. To browse through the table you can click the links '''<<first''', '''<<prev''', '''next>>''' and '''last>>'''. The links only appear if there is e.g. a next page. The text in the middle of the links will tell you which items are currently displayed. [[Image:TableBrowse.png]] === Sorting === You can sort the contents of the table by each column using the little arrows next to the column header. The sorting is done using JavaScript, meaning that it does not reload the page. [[Image:TableSort.png]] === Filtering === Different kinds of filters can be applied to the table data. The table always uses all filters for all columns at once. This means that if you may want to check if other filters are active, if the result of filtering a column is not what you expect. Often, a '''clear all filters''' button is made available on top of the page. One filter is simply a text field that does an infix search (meaning that if the word you type in the text field is part of a word in the cells of a cell in the respective column, the row will be visible). [[Image:TableFilter1.png]] The combo box filter is usually used if only a small number of different values are used in a column. These values appear in the combo box if you click the arrow next to the textfield. Choose one and the table will filter automatically. [[Image:TableFilter2.png]] If a column consists of numbers, you will often get a filter using operators ('''>''', '''<''', '''=''' and others). You can choose one of these operators, and put a number into the text field below the operator to filter the table. [[Image:TableFilter3.png]] === Export === dbe952c142c000444378ae3d26dda0444308b745 2147 2146 2008-11-26T11:06:07Z DanielaBartels 10 /* Export */ wikitext text/x-wiki == Table == The Table component has a large number of functionalities that can be used to access data that can be displayed in tabular form. Features of the table component are '''Browsing''', '''Sorting''', '''Filtering''' and '''Export'''. Most of these functions of the table are implemented by JavaScript functions. That means, it does not lead to a reload of the page. The page ''knows'' all the information, but only part of it is displayed. The display is then manipulated using JavaScript functions. A table consists of a header row (here in dark blue) and the rows that contain the data. In some cases the header row can be supplied with a supercolumn to group columns. The header cells contain the functionality to sort and filter the row data, as described below. The rows are colored in two different colors for better visibility (here white and light grey background). If you hover over a row, it will be highlighted in dark grey. [[Image:Table1.png]] === Browsing === The number of rows you want your table to display at once can be changed using the text box '''display ___ items per page'''. Just press return after changing the number to change the display of your table. To browse through the table you can click the links '''<<first''', '''<<prev''', '''next>>''' and '''last>>'''. The links only appear if there is e.g. a next page. The text in the middle of the links will tell you which items are currently displayed. [[Image:TableBrowse.png]] === Sorting === You can sort the contents of the table by each column using the little arrows next to the column header. The sorting is done using JavaScript, meaning that it does not reload the page. [[Image:TableSort.png]] === Filtering === Different kinds of filters can be applied to the table data. The table always uses all filters for all columns at once. This means that if you may want to check if other filters are active, if the result of filtering a column is not what you expect. Often, a '''clear all filters''' button is made available on top of the page. One filter is simply a text field that does an infix search (meaning that if the word you type in the text field is part of a word in the cells of a cell in the respective column, the row will be visible). [[Image:TableFilter1.png]] The combo box filter is usually used if only a small number of different values are used in a column. These values appear in the combo box if you click the arrow next to the textfield. Choose one and the table will filter automatically. [[Image:TableFilter2.png]] If a column consists of numbers, you will often get a filter using operators ('''>''', '''<''', '''=''' and others). You can choose one of these operators, and put a number into the text field below the operator to filter the table. [[Image:TableFilter3.png]] === Export === For most table, you will find an '''export''' button on the page. This will let you download the data of the table in '''.tsv''' format. This tab-separated text can be opened with many Editors, or Excel. 603ad836afc6f13cf03fae086d773d2ee6dc4184 6 1527 2132 2008-11-26T09:35:39Z DanielaBartels 10 wikitext text/x-wiki da39a3ee5e6b4b0d3255bfef95601890afd80709 6 1528 2133 2008-11-26T09:37:03Z DanielaBartels 10 wikitext text/x-wiki da39a3ee5e6b4b0d3255bfef95601890afd80709 6 1529 2135 2008-11-26T09:39:50Z DanielaBartels 10 wikitext text/x-wiki da39a3ee5e6b4b0d3255bfef95601890afd80709 6 1530 2136 2008-11-26T09:49:45Z DanielaBartels 10 wikitext text/x-wiki da39a3ee5e6b4b0d3255bfef95601890afd80709 6 1531 2142 2008-11-26T10:36:38Z DanielaBartels 10 wikitext text/x-wiki da39a3ee5e6b4b0d3255bfef95601890afd80709 0 1532 2148 2008-11-26T11:07:08Z DanielaBartels 10 wikitext text/x-wiki [[WebComponents/Table|Table]] [[WebComponents/Table|Tabview]] 1fc1972e82039e23369e3c17657d892f74ac7bca 2166 2148 2008-11-26T14:14:29Z DanielaBartels 10 wikitext text/x-wiki [[WebComponents/Login|Login]] [[WebComponents/Table|Table]] [[WebComponents/TabView|Tabview]] 4c1867c25bb17d4ab50c73bcb697f4b19949d415 2167 2166 2008-11-26T14:14:46Z DanielaBartels 10 wikitext text/x-wiki [[WebComponents/Login|Login]] [[WebComponents/Table|Table]] [[WebComponents/Tabview|TabView]] 22b07a8adade7c74542800791ae67bead655f668 2168 2167 2008-11-26T14:15:15Z DanielaBartels 10 wikitext text/x-wiki [[WebComponents/Login|LoginBox]] [[WebComponents/Table|Table]] [[WebComponents/Tabview|TabView]] e6fec1eb6be178a58ccc1a855bd2447165f3b210 0 1533 2149 2008-11-26T11:38:05Z DanielaBartels 10 wikitext text/x-wiki == Find == 9537c53e20f7960b430777c9438f27e85ca2e751 2150 2149 2008-11-26T11:42:47Z DanielaBartels 10 /* Find */ wikitext text/x-wiki == Find == The Find Window is present on every page in the SeedViewer. Type in a text and press the button '''Find''' to search for your keyword. [[Image:FindWindow]] 04ef16465c669c2990037a80a513f9e794ca9e0b 2153 2150 2008-11-26T11:43:32Z DanielaBartels 10 /* Find */ wikitext text/x-wiki == Find == The Find Window is present on every page in the SeedViewer. Type in a text and press the button '''Find''' to search for your keyword. [[Image:FindWindow.png]] dd727da20ab06b3c3ce4a5467593d94d17229a76 2154 2153 2008-11-26T11:58:05Z DanielaBartels 10 /* Find */ wikitext text/x-wiki == Find == The Find Window is present on every page in the SeedViewer. Type in a text and press the button '''Find''' to search for your keyword. [[Image:FindWindow.png]] === What it does === The given keyword is used to first search different categories in the SEED database for a perfect match (fast search) in the following order: Subsystems Organisms Feature IDs If a perfect match is found, it returns the page for that match in that category (e.g. if you search for Escherichia coli K12, the SeedViewer will load the [[SEED_Viewer_Manual/OrganismPage|Organism Page]] for that organism. If no perfect match is found, the listed categories will be searched again using an infix search (meaning that the keyword can be part of an organism, functional role etc.). The infix search may take a while. You will get a list 2bde5b748f9eebc4c5a51caf9c2a9b733fc7f595 2155 2154 2008-11-26T12:13:14Z DanielaBartels 10 /* What it does */ wikitext text/x-wiki == Find == The Find Window is present on every page in the SeedViewer. Type in a text and press the button '''Find''' to search for your keyword. [[Image:FindWindow.png]] === What it does === The given keyword is used to first search different categories in the SEED database for a perfect match (fast search) in the following order: Subsystems Organisms Feature IDs If a perfect match is found, it returns the page for that match in that category (e.g. if you search for Escherichia coli K12, the SeedViewer will load the [[SEED_Viewer_Manual/OrganismPage|Organism Page]] for that organism. If no perfect match is found, the listed categories will be searched again using an infix search (meaning that the keyword can be part of an organism, functional role etc.). The infix search may take a while. You will get a page that lists all search results for your search. === Special features === If your page has a defined genome (e.g. [[SEED_Viewer_Manual/OrganismPage|Organism Page]], [[SEED_Viewer_Manual/Annotation|Annotation Page]], you can type in a number and it will open the Annotation page for the feature ending with that number. This is helpfull when you want to browse through Annotation pages of many features in a genome. 4f7db7b59540b19348074188406bd3fac221a967 2156 2155 2008-11-26T12:13:36Z DanielaBartels 10 /* Special features */ wikitext text/x-wiki == Find == The Find Window is present on every page in the SeedViewer. Type in a text and press the button '''Find''' to search for your keyword. [[Image:FindWindow.png]] === What it does === The given keyword is used to first search different categories in the SEED database for a perfect match (fast search) in the following order: Subsystems Organisms Feature IDs If a perfect match is found, it returns the page for that match in that category (e.g. if you search for Escherichia coli K12, the SeedViewer will load the [[SEED_Viewer_Manual/OrganismPage|Organism Page]] for that organism. If no perfect match is found, the listed categories will be searched again using an infix search (meaning that the keyword can be part of an organism, functional role etc.). The infix search may take a while. You will get a page that lists all search results for your search. === Special features === If your page has a defined genome (e.g. [[SEED_Viewer_Manual/OrganismPage|Organism Page]], [[SEED_Viewer_Manual/Annotation|Annotation Page]]), you can type in a number and it will open the Annotation page for the feature ending with that number. This is helpful when you want to browse through Annotation pages of many features in a genome. 871b21c1fdf58ae3afd50af17f9974a63872f4b8 2157 2156 2008-11-26T12:27:41Z DanielaBartels 10 /* Find */ wikitext text/x-wiki == Find == The Find Window is present on every page in the SeedViewer. Type in a text and press the button '''Find''' to search for your keyword. [[Image:FindWindow.png]] === What it does === The given keyword is used to first search different categories in the SEED database for a perfect match (fast search) in the following order: Organisms Subsystems Feature IDs Aliases to Features If a perfect match is found, it returns the page for that match in that category (e.g. if you search for Escherichia coli K12, the SeedViewer will load the [[SEED_Viewer_Manual/OrganismPage|Organism Page]] for that organism. If no perfect match is found, the listed categories will be searched again using an infix search (meaning that the keyword can be part of an organism, functional role etc.). The infix search may take a while. You will get a page that lists all search results for your search. === Special features === If your page has a defined genome (e.g. [[SEED_Viewer_Manual/OrganismPage|Organism Page]], [[SEED_Viewer_Manual/Annotation|Annotation Page]]), you can type in a number and it will open the Annotation page for the feature ending with that number. This is helpful when you want to browse through Annotation pages of many features in a genome. 5980fbae1d6feb83f56e5571ca2d8743ba7ab29e 2158 2157 2008-11-26T12:28:50Z DanielaBartels 10 /* Special features */ wikitext text/x-wiki == Find == The Find Window is present on every page in the SeedViewer. Type in a text and press the button '''Find''' to search for your keyword. [[Image:FindWindow.png]] === What it does === The given keyword is used to first search different categories in the SEED database for a perfect match (fast search) in the following order: Organisms Subsystems Feature IDs Aliases to Features If a perfect match is found, it returns the page for that match in that category (e.g. if you search for Escherichia coli K12, the SeedViewer will load the [[SEED_Viewer_Manual/OrganismPage|Organism Page]] for that organism. If no perfect match is found, the listed categories will be searched again using an infix search (meaning that the keyword can be part of an organism, functional role etc.). The infix search may take a while. You will get a page that lists all search results for your search. === Special features === If your page has a defined genome (e.g. [[SEED_Viewer_Manual/OrganismPage|Organism Page]], [[SEED_Viewer_Manual/Annotation|Annotation Page]]), you can type in a number and it will open the Annotation page for the feature ending with that number. This is helpful if you want to browse through Annotation pages of many features in a genome. 822e5b58894cc16cd604428fed4b50ca067eb43f 2159 2158 2008-11-26T12:32:47Z DanielaBartels 10 /* What it does */ wikitext text/x-wiki == Find == The Find Window is present on every page in the SeedViewer. Type in a text and press the button '''Find''' to search for your keyword. [[Image:FindWindow.png]] === What it does === The given keyword is used to first search different categories in the SEED database for a perfect match (fast search) in the following order: Organisms Subsystem Names Feature IDs Aliases to Features If a perfect match is found, it returns the page for that match in that category (e.g. if you search for Escherichia coli K12, the SeedViewer will load the [[SEED_Viewer_Manual/OrganismPage|Organism Page]] for that organism. If no perfect match is found, it will search the following categories using an infix search (meaning that the keyword can be part of an organism, functional role etc.): Functional Roles Organisms Subsystem Names Feature Annotations The infix search may take a while. You will get a page that lists all search results for your search. === Special features === If your page has a defined genome (e.g. [[SEED_Viewer_Manual/OrganismPage|Organism Page]], [[SEED_Viewer_Manual/Annotation|Annotation Page]]), you can type in a number and it will open the Annotation page for the feature ending with that number. This is helpful if you want to browse through Annotation pages of many features in a genome. df4b9d2d8395e5f5234e5d4b84cc570f66db3848 2160 2159 2008-11-26T12:33:22Z DanielaBartels 10 /* Find */ wikitext text/x-wiki == Find == The Find Window is present on every page in the SeedViewer. Type in a text and press the button '''Find''' to search for your keyword. [[Image:FindWindow.png]] === What it does === The given keyword is used to first search different categories in the SEED database for a perfect match (fast search) in the following order: - Organisms - Subsystem Names - Feature IDs - Aliases to Features If a perfect match is found, it returns the page for that match in that category (e.g. if you search for Escherichia coli K12, the SeedViewer will load the [[SEED_Viewer_Manual/OrganismPage|Organism Page]] for that organism. If no perfect match is found, it will search the following categories using an infix search (meaning that the keyword can be part of an organism, functional role etc.): - Functional Roles - Organisms - Subsystem Names - Feature Annotations The infix search may take a while. You will get a page that lists all search results for your search. === Special features === If your page has a defined genome (e.g. [[SEED_Viewer_Manual/OrganismPage|Organism Page]], [[SEED_Viewer_Manual/Annotation|Annotation Page]]), you can type in a number and it will open the Annotation page for the feature ending with that number. This is helpful if you want to browse through Annotation pages of many features in a genome. 26ec14a89e4eda7fbc4b07ecbad471d3032b6684 2161 2160 2008-11-26T12:33:44Z DanielaBartels 10 /* What it does */ wikitext text/x-wiki == Find == The Find Window is present on every page in the SeedViewer. Type in a text and press the button '''Find''' to search for your keyword. [[Image:FindWindow.png]] === What it does === The given keyword is used to first search different categories in the SEED database for a perfect match (fast search) in the following order: - Organisms - Subsystem Names - Feature IDs - Aliases to Features If a perfect match is found, it returns the page for that match in that category (e.g. if you search for Escherichia coli K12, the SeedViewer will load the [[SEED_Viewer_Manual/OrganismPage|Organism Page]] for that organism. If '''no''' perfect match is found, it will search the following categories using an infix search (meaning that the keyword can be part of an organism, functional role etc.): - Functional Roles - Organisms - Subsystem Names - Feature Annotations The infix search may take a while. You will get a page that lists all search results for your search. === Special features === If your page has a defined genome (e.g. [[SEED_Viewer_Manual/OrganismPage|Organism Page]], [[SEED_Viewer_Manual/Annotation|Annotation Page]]), you can type in a number and it will open the Annotation page for the feature ending with that number. This is helpful if you want to browse through Annotation pages of many features in a genome. fb285e9a3919777ddd64789d9fb6030bb755c933 0 1524 2151 2125 2008-11-26T11:42:53Z TobiasPaczian 17 /* The TabView */ wikitext text/x-wiki == The TabView == The TabView component is used on many pages in the [[SEED_Viewer_Manual|SeedViewer]]. It is useful at places where you have different options to access data or you need to fulfill a task step-by-step. The entire content of the TabView is loaded when you enter the page. Clicking a different tab only displays the data which was hidden before. At the top of the TabView, you can access the different tabs. In the example (SeedViewer Mainpage), the chosen tab is white, while all hidden tabs have a green header. Click on the green header to activate the respective tab. [[Image:TabView.png]] fd59f9ac0ab55f0ca1546c6a85b7316d3e26c5d0 6 1534 2152 2008-11-26T11:43:11Z DanielaBartels 10 wikitext text/x-wiki da39a3ee5e6b4b0d3255bfef95601890afd80709 0 1367 2162 2013 2008-11-26T14:09:45Z DanielaBartels 10 wikitext text/x-wiki === Aliases === Usually used in context of feature IDs. They are database crossreferences. === Annotators SEED === The master copy for all data in the SEED environment. Users can not access this password protected site. All annotations are made available via the [[#SEED-Viewer| SEED-Viewer]] and the [[#Trial-SEED|Trial-SEED]]. === Annotation === please see [[#Assigning_a_gene_function_and_annotation| Assigning a gene function and annotation]] === Assigning a gene function and annotation === Annotators assign gene functions to genes, and we call this process annotation. In most contexts, people use the term annotation to refer to assignments of function to the genes within a single organism. We certainly use the term in this sense, but we also use it to describe the process of assigning functions to corresponding genes from numerous genomes. Our basic approach to annotation is to ask our annotators to annotate the genes included in a [[#subsystem|Subsystem]] (e.g., glycolysis) across all genomes. This process of annotation of the genes within a subsystem across a set of genomes, rather than annotation of genes within a single genome, allows our annotators to focus on a constrained set of functional roles and attempt to accurately identify exactly what variant, if any, of a subsystem exists in each of the genomes. We use the term annotation to refer to assigning functions to genes (either within a single organism or to a constrained set of gene/protein families across a set of organisms). This activity certainly is closely related to the construction of subsystems and protein families (which we call FIGfams), but we will describe those activities elsewhere. === Assignment === please see [[#Assigning_a_gene_function_and_annotation| Assigning a gene function and annotation]] === Bidirectional Best Hit (BBH) === The paper [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=EBI&pubmedid=10077608 The use of gene clusters to infer functional coupling] defines a Bidirectional Best Hit or BBH as follows: <blockquote> Given two genes Xa and Xb from two genomes Ga and Gb, Xa and Xb are called a “bidirectional best hit (BBH)” if and only if recognizable similarity exists between them (in our case, we required fasta3 scores lower than 1.0 × 10−5), there is no gene Zb in Gb that is more similar than Xb is to Xa, and there is no gene Za in Ga that is more similar than Xa is to Xb. Genes (Xa, Ya) from Ga and (Xb, Yb) from Gb form a “pair of close bidirectional best hits (PCBBH)” if and only if Xa and Ya are close, Xb and Yb are close, Xa and Xb are a BBH, and Ya and Yb are a BBH. </blockquote> === Clearinghouse === please see [[#SubsystemClearinghouse|Subsystem Clearinghouse]] ===Feature=== A feature is a defined region in the DNA. A PEG is the most prevalent feature type in the SEED. Some other feature types include RNA, prophage and pathogenicity islands. The format for a feature ID is fig|genome_id.feature_abbreviation.feature_number (ie fig|83333.1.peg.100 ). === FIGfam === FIGfams are protein families generated by the Fellowship for Interpretation of Genomes (FIG). These families are based on the collection of subsystems, as well as correspondences between genes in closely related strains (we describe the construction of FIGfams in a separate SOP). The important properties of these families are as follows: # Two PEGs which both occur within a single FIGfam are believed to have the same function. # There is a decision procedure associated with the family which can be invoked to determine whether or not a gene can be “safely” assigned the function associated with the family. === FIG Identifier / FIG-IDs === We provide identifiers for genome sequences and features in the following form: {| ! Entity type !! key !! identifier |- | Genome || genome || fig<nowiki>|</nowiki>83331.1 |- | PEG || id || fig<nowiki>|</nowiki>83331.peg.123 |- | RNA feature || id || fig<nowiki>|</nowiki>83331.rna.1 |- |} (Please also see below for information on how to link to the SEED.) === Functional coupling === The availability of multiple genomes provides an opportunity to gain new insights into the processes that drive the dispersion and formation of chromosomal gene clusters. The paper [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=EBI&pubmedid=10077608 The use of gene clusters to infer functional coupling] describes a method to compute functional coupling of features due to conserved gene clusters . === Functional role === The concept of functional role is both basic and primitive in the sense that we will not pretend to offer a precise definition. It corresponds roughly to a single logical role that a gene or gene product may play in the operation of a cell. === Gene function === The function of a protein-encoding gene (PEG) is the functional role played by the product of the gene or an expression describing a set of roles played by the encoded protein. The operators used to construct expressions and the meanings associated with the operators are described in http://www.nmpdr.org/FIG/Html/SEED_functions.html Genes other than PEGs can also be assigned functions (e.g., SSU rRNA). However, in most cases the functions assigned to genes other than PEGs tend not to be problematic. === Linking to the SEED === We support linking to the SEED using a generic mechanism: Base URL: http://www.theseed.org/linkin.cgi? {| |+ Supported SEED Identifiers for external use ! Entity type !! key !! identifier !! Example |- | Genome || genome || fig<nowiki>|</nowiki>83331.1 || [[http://www.theseed.org/linkin.cgi?genome=fig|83333.1 http://www.theseed.org/linkin.cgi?genome=fig&#124;83333.1]] |- | PEG || id || fig<nowiki>|</nowiki>83331.peg.123 || [[http://www.theseed.org/linkin.cgi?id=fig|83333.1.peg.123 http://www.theseed.org/linkin.cgi?id=fig&#124;83333.1.peg.123]] |- | RNA feature || id || fig<nowiki>|</nowiki>83331.rna.1 || [[http://www.theseed.org/linkin.cgi?id=fig|83333.1.rna.1 http://www.theseed.org/linkin.cgi?id=fig&#124;83333.1.rna.1]] |- |} SEED identifiers contain the NCBI taxonomy ID, thus if the taxonomy ID changes, we need to update our internal data accordingly. To provide stable external identifiers, we keep a list of IDs that have changed and display warning message informing the user of the change and provide a link to the new version of the data requested. === Metabolic Reconstruction === When we use the term metabolic reconstruction of a given genome we will simply mean the set of populated subsystems that contain the genome, the PEGs (and their assigned functions) that are connected to functional roles in these populated subsystems, and the specific variant code associated with the genome in each of the populated subsystems. === NMPDR pathogen genome === The NMPDR is responsible for five classes of genomes: # Campylobacter jejuni # Listeria monocytogenes # Staphylococcus aureus # Streptococcus pneumoniae and Streptococcus pyogenes # Pathogenic Vibrio === Pair of Close Homologs (PCH) === The paper [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=EBI&pubmedid=10077608 The use of gene clusters to infer functional coupling] defines a Pair of Close Homologs as follows: <blockquote> We can also define the concept of “pairs of close homologs” (PCHs) as follows: genes (X′a, Y′a) from Ga and (X′b, Y′b) from Gb form a PCH if and only if X′a and Y′a are close, X′b and Y′b are close, X′a and X′b are recognizably similar, and Y′a and Y′b are recognizably similar. Here, we will consider two genes to be recognizably similar if their gene products produce fasta3 scores lower than 1.0 × 10−5. We use a scoring scheme analogous to the one described for PCBBHs to evaluate the connections between PCHs, except that if Ga and Gb are the same genome, we assign an arbitrary “same-genome score” (“same-genome” pairs cannot occur for PCBBHs by definition, but for PCHs they are possible). Unlike PCBBHs from two very close genomes for which contiguity is completely uninformative in the vast majority of cases, PCHs allow recognition of gene clusters that play similar (but usually not identical) roles (such as two transport cassettes containing pairs of homologs) in the same or similar organisms. The arbitrary “same-genome score” should, we believe, have a value that is high enough to rank such instances as significant. </blockquote> === PEG === A Protein Encoding Gene (PEG) is equivalent to a CDS (Coding Sequence). === Populated Subsystem === please see [[#Subsystem|Subsystem]] === RAST === RAST or Rapid Annotation using Subsystem Technology is a rapid and very accurate annotation technology. We make a RAST server available for public use at http://rast.nmpdr.org === SEED-Viewer === The SEED Viewer is a web-based application that allows browsing of SEED data structures. We use the SEED-Viewer to provide a public read-only version of the latest SEED data at: http://seed-viewer.theseed.org '''Please note''': The data is updated automatically every 24 hours. When citing or linking to the SEED please use this version. === Subsystem === A subsystem is a set of functional roles that an annotator has decided should be thought of as related. Frequently, subsystems represent the collection of [[#Functional_role|functional roles]] that make up a metabolic pathway, a complex (e.g., the ribosome), or a class of proteins (e.g., two-component signal-transduction proteins within Staphylococcus aureus). A '''populated subsystem''' is a subsystem with an attached spreadsheet. The rows of the spreadsheet represent genomes and the columns represent the functional roles of the spreadsheet. Each cell contains the identifiers of genes from the corresponding genome the implement the specific functional role. That is, a populated subsystem specifies which genes implement instances of the subsystem in each of the genomes. The rows of a populated genome are assigned '''variant codes''' which describe which of a set of possible variants of the subsystem exist within each genome (special codes expressing a total absence of the subsystem or remaining uncertainty exist). Construction of a large set of curated populated subsystems is at the center of the NMPDR and SEED annotation efforts. === Subsystem Clearing House === Since annotators can work on any machine (including the public SEED) the way to propagate subsystems is via http://clearinghouse.theseed.org/clearinghouse_browser.cgi? === Trial-SEED === A public, read-write copy of the SEED is made available on http://theseed.uchicago.edu/FIG/index.cgi '''Please note''': The data on this server is updated in irregular intervals. Users should not assume that annotations made on this system will persist. Please publish your annotations to the [[#Subsystem_clearing_house|Subsystem Clearing house]]. === Variant Code=== please see [[#Subsystem|Subsystem]] 2114b281246bacb012a292a0a473bde414939df1 0 1463 2163 2095 2008-11-26T14:10:11Z DanielaBartels 10 /* (4) Body of the Page */ wikitext text/x-wiki The SEED is a framework to support comparative analysis and annotation of genomes. The SEED Viewer allows you to explore the curated genomes that have been produced by a cooperative effort that includes Fellowship for Interpretation of Genomes (FIG), Argonne National Laboratory, the University of Chicago and teams from a number of other institutions. These pages will cover the usage of the different pages within the Seed Viewer. An overview of the main pages in the SeedViewer can be found in the '''[[SEED_Viewer_Manual/Contents|Contents Page]]'''. == Home == The home page of the seedviewer offers you several entry points to explore the data in the [[Home_of_the_SEED|SEED]]. Common components of a web page in the seedviewer are the following. The image below depicts the locations of the components: === (1) [[SEED_Viewer_Manual/Menu|The menu]] === Hovering over the menu will show you submenus that are relevant for the page you are viewing. The categories '''[[SEED_Viewer_Manual/Menu#Navigate_Menu|Navigate]]''' and '''[[SEED_Viewer_Manual/Menu#Help_Menu|Help]]''' will always be present on each page. Other menu categories are added dependent on the context of the page. Click [[SEED_Viewer_Manual/Menu|here]] to learn more about using the menu. === (2) [[SEED_Viewer_Manual/Find|Find Window]] === The Find window allows you to search for keywords or ids. To learn more about the find window, click [[SEED_Viewer_Manual/Find|here]]. === (3) [[WebComponents/Login|Login Box]] === Some actions may require a user to get a user account and log in. This is necessary for viewing private organisms a user has uploaded to the [[RAST_Tutorial|RAST]]. You can create a login by clicking on '''Register''' in the '''Help''' menu. To learn more about user management click [[SEED_Viewer_Manual/UserManagement|here]]. === (4) Body of the Page === The home page allows you to specifically search the SEED data using five categories. They are presented in a [[WebComponents/Tabview|TabView]] at the bottom of the Home page: '''a) Organisms''' Select an organism of interest in the [[SEED_Viewer_Manual/OrganismSelect|Organism Select]] and press the button '''select'''. This will lead to the [[SEED_Viewer_Manual/OrganismPage|Organism Page]] of that organism. '''b) Subsystems''' Selecting a subsystem in the Select Box and clicking '''Select''' will lead you to a [[SEED_Viewer_Manual/Subsystems|Subsystem Page]]. You can narrow the selection by typing in a part of the subsystem name into the field on top of the select box. '''c) ID search''' If you know the ID of a gene or protein you're interested in, you can directly type it into this field and press '''ID Search'''. The ID can be a SEED (fig) id as well as many other types of IDs from other databases (e.g. GenBank, KEGG, SwissProt, UniProt and others). These IDs are saved in the SEED as [[Glossary#Aliases|Aliases]]. '''d) Text search''' You can search for any type of data in this field. This includes search for Organisms, Subsystems, IDs as well as Functional Roles of proteins. It should be used carefully, as the search is an infix search and can take very long (e.g. if you only type in one letter it may take forever). If you already know that you are looking for, e.g. a subsystem, it would be faster to use the Subsystems tab. '''e) BLAST''' This tab offers the option to search a DNA or protein sequence against an organism in the SEED. It is described in more detail [[SEED_Viewer_Manual/BLASTOrganism|here]]. [[Image:Home1.png]] 83636cd7bbeea44d95cb23fa49cf97129e3244d5 0 1535 2164 2008-11-26T14:12:30Z DanielaBartels 10 wikitext text/x-wiki == Login Box == [[Image:LoginBox.png]] dfe51c2da32b246a3159d4a48d2080deb1726fa1 2169 2164 2008-11-26T14:21:35Z DanielaBartels 10 /* Login Box */ wikitext text/x-wiki == Login Box == If you have a User Login for SEED applications (SeedViewer, RAST, MetaRAST and others), you can easily log in using the Login Box present on the right side of the menu page on every page (unless you are already logged in). After logging in, the Login Box will be replaced by your first and last name. [[Image:LoginBox.png]] c3d7c19c4072ef2e55aad1d4e14e436cd8367848 2170 2169 2008-11-26T14:23:08Z DanielaBartels 10 /* Login Box */ wikitext text/x-wiki == Login Box == If you have a User Login for SEED applications (SeedViewer, RAST, MetaRAST and others), you can easily log in using the Login Box present on the right side of the menu page on every page (unless you are already logged in). Enter your login in the first textbox, and your password in the second, then press return. [[Image:LoginBox.png]] After logging in, the Login Box will be replaced by your first and last name. 77a41148ce9da0d4e2bdc898c9b8d9548cc26d32 2171 2170 2008-11-26T14:26:27Z DanielaBartels 10 /* Login Box */ wikitext text/x-wiki == Login Box == If you have a User Login for SEED applications (SeedViewer, RAST, MetaRAST and others), you can easily log in using the Login Box present on the right side of the menu page on every page (unless you are already logged in). Enter your login in the first textbox, and your password in the second, then press return. [[Image:LoginBox.png]] After logging in, the Login Box will be replaced by your first and last name. If you don't have a login yet, but you wish to use applications or functions a login is required for (e.g. upload a genome to the [[RAST_Tutorial|RAST]], use the link '''Register''' in the '''[[SEED_Viewer_Manual/Menu#Help|Help Menu]]'''. 0a374646a06ff7aee999634fdde39a620c566ec7 2172 2171 2008-11-26T14:27:00Z DanielaBartels 10 /* Login Box */ wikitext text/x-wiki == Login Box == If you have a User Login for SEED applications (SeedViewer, RAST, MetaRAST and others), you can easily log in using the Login Box present on the right side of the menu page on every page (unless you are already logged in). Enter your login in the first textbox, and your password in the second, then press return. [[Image:LoginBox.png]] After logging in, the Login Box will be replaced by your first and last name. If you don't have a login yet, but you wish to use applications or functions a login is required for (e.g. upload a genome to the [[RAST_Tutorial|RAST]], use the link '''Register''' in the '''[[SEED_Viewer_Manual/Menu#Help Menu|Help Menu]]'''. 7e8c586c1ca301cb633ecbcab10b494e96bb233f 2173 2172 2008-11-26T14:27:27Z DanielaBartels 10 /* Login Box */ wikitext text/x-wiki == Login Box == If you have a User Login for SEED applications (SeedViewer, RAST, MetaRAST and others), you can easily log in using the Login Box present on the right side of the menu page on every page (unless you are already logged in). Enter your login in the first textbox, and your password in the second, then press return. [[Image:LoginBox.png]] After logging in, the Login Box will be replaced by your first and last name. If you don't have a login yet, but you wish to use applications or functions a login is required for (e.g. upload a genome to the [[RAST_Tutorial|RAST]]), use the link '''Register''' in the '''[[SEED_Viewer_Manual/Menu#Help Menu|Help Menu]]'''. 7f96a195c9bb67eefc7ae6ae8d3d496577085bb6 2176 2173 2008-11-26T14:55:46Z DanielaBartels 10 /* Login Box */ wikitext text/x-wiki == Login Box == If you have a User Login for SEED applications (SeedViewer, RAST, MetaRAST and others), you can easily log in using the Login Box present on the right side of the menu page on every page (unless you are already logged in). Enter your login in the first textbox, and your password in the second, then press return. [[Image:LoginBox.png]] After logging in, the Login Box will be replaced by your first and last name, together with the small items displayed below. The little door icon lets you log out. The other icon leads to your [[SEED_Viewer_Manual/UserManagement|User Management Page]]. [[Image:LoginIcons.png]] If you don't have a login yet, but you wish to use applications or functions a login is required for (e.g. upload a genome to the [[RAST_Tutorial|RAST]]), use the link '''Register''' in the '''[[SEED_Viewer_Manual/Menu#Help Menu|Help Menu]]'''. 10cc6f97ad7f9ab0ed589a942a32227b0aa95f2f 2178 2176 2008-11-26T15:02:20Z DanielaBartels 10 /* Login Box */ wikitext text/x-wiki == Login Box == If you have a User Login for SEED applications (SeedViewer, RAST, MetaRAST and others), you can easily log in using the Login Box present on the right side of the menu page on every page (unless you are already logged in). Enter your login in the first textbox, and your password in the second, then press return. [[Image:LoginBox.png]] After logging in, the Login Box will be replaced by your first and last name, together with the small items displayed below. The little door icon lets you log out. The other icon leads to your [[SEED_Viewer_Manual/UserManagement|User Management Page]]. [[Image:LoginIcons.png]] If you don't have a login yet, but you wish to use applications or functions a login is required for (e.g. upload a genome to the [[RAST_Tutorial|RAST]]), use the link '''[[SEED_Viewer_Manual/Register|Register]]''' in the '''[[SEED_Viewer_Manual/Menu#Help Menu|Help Menu]]'''. 9bcf5e977e3bfbd751438d3a262897ea4c89a952 6 1536 2165 2008-11-26T14:12:49Z DanielaBartels 10 wikitext text/x-wiki da39a3ee5e6b4b0d3255bfef95601890afd80709 0 1537 2174 2008-11-26T14:52:30Z DanielaBartels 10 wikitext text/x-wiki == User Management == [[Image:UserManagement.png]] 3d32d8ff08ea41b4823136147fd623d8986b3081 2179 2174 2008-11-26T15:16:29Z DanielaBartels 10 /* User Management */ wikitext text/x-wiki == User Management == The user management page offers options to change your user information (first name, last name, email and password). Click '''perform changes''' to save your changes. The password has to be typed in twice to avoid typing errors. [[Image:UserManagement.png]] ac420c1e329161abb81288f2cc962dc0099db04f 6 1538 2175 2008-11-26T14:52:48Z DanielaBartels 10 wikitext text/x-wiki da39a3ee5e6b4b0d3255bfef95601890afd80709 6 1539 2177 2008-11-26T14:56:15Z DanielaBartels 10 wikitext text/x-wiki da39a3ee5e6b4b0d3255bfef95601890afd80709 0 1537 2180 2179 2008-11-26T15:32:58Z DanielaBartels 10 /* User Management */ wikitext text/x-wiki == User Management == The user management page offers options to change your user information (first name, last name, email and password). Click '''perform changes''' to save your changes. The password has to be typed in twice to avoid typing errors. The section '''Your Group Memberships''' lists user groups you are part of. A user group is build if a right should be added to a whole group of people, e.g. a group of people annotating a genome. Click on the link to view all members of a group. [[Image:UserManagement.png]] 8bfe672449bf2c3a45f26f35ea8ba76e8be9ccc2 0 1540 2181 2008-11-26T15:50:19Z DanielaBartels 10 wikitext text/x-wiki == Register == Registering for a service (RAST, MetaRAST, or others) can be done using this registry form. Use the first tab of the [[WebComponents/Tabview|TabView]] to register if you have not already got an account for an other service. If you already have an account (for example, you have a user login for the RAST, but now you need access to the MetaRAST), use the second tab, where you only have to state your login and email to register for this service. Put in your personal information and click the button '''Request'''. An administrator will check your request and send you a user login or give you access to the requested service. [[Image:Register.png]] aa625f666275eed6d88d19ed1ab317d4c16c09fa 6 1541 2182 2008-11-26T15:50:36Z DanielaBartels 10 wikitext text/x-wiki da39a3ee5e6b4b0d3255bfef95601890afd80709 0 1466 2183 2121 2008-11-26T16:12:34Z DanielaBartels 10 /* Main pages of the SeedViewer */ wikitext text/x-wiki == Main pages of the SeedViewer == ''' [[SEED_Viewer_Manual|Home Page]] ''' ''' [[SEED_Viewer_Manual/Menu|Menu]] ''' ''' [[SEED_Viewer_Manual/SubsystemSelect|Subsystem Select]] ''' '''[[SEED_Viewer_Manual/Subsystems|Subsystems]]''' '''[[SEED_Viewer_Manual/FunctionaRole|Functional Role]]''' '''[[SEED_Viewer_Manual/FIGfamViewer|FIGfam Viewer]]''' '''[[SEED_Viewer_Manual/Annotation|Annotation]]''' '''[[SEED_Viewer_Manual/Evidence|Evidence]]''' '''[[SEED_Viewer_Manual/BLASTOrganism|BLAST against an organism]]''' '''[[SEED_Viewer_Manual/ShowSeqs|Sequence]]''' '''[[SEED_Viewer_Manual/GenomeBrowser|Browse Genome]]''' '''[[SEED_Viewer_Manual/OrganismSelect|Organism Select]]''' '''[[SEED_Viewer_Manual/OrganismPage|Organism Page]]''' '''[[SEED_Viewer_Manual/KEGG|KEGG]]''' '''[[SEED_Viewer_Manual/HomologClusters|Homolog Clusters]]''' f014111a487e0d6325712ac904d5673d9de0796d 2189 2183 2008-11-26T16:59:49Z DanielaBartels 10 /* Main pages of the SeedViewer */ wikitext text/x-wiki == Main pages of the SeedViewer == ''' [[SEED_Viewer_Manual|Home Page]] ''' ''' [[SEED_Viewer_Manual/Menu|Menu]] ''' ''' [[SEED_Viewer_Manual/SubsystemSelect|Subsystem Select]] ''' '''[[SEED_Viewer_Manual/Subsystems|Subsystems]]''' '''[[SEED_Viewer_Manual/FunctionaRole|Functional Role]]''' '''[[SEED_Viewer_Manual/FIGfamViewer|FIGfam Viewer]]''' '''[[SEED_Viewer_Manual/Annotation|Annotation]]''' '''[[SEED_Viewer_Manual/Evidence|Evidence]]''' '''[[SEED_Viewer_Manual/BLASTOrganism|BLAST against an organism]]''' '''[[SEED_Viewer_Manual/ShowSeqs|Sequence]]''' '''[[SEED_Viewer_Manual/GenomeBrowser|Browse Genome]]''' '''[[SEED_Viewer_Manual/OrganismSelect|Organism Select]]''' '''[[SEED_Viewer_Manual/OrganismPage|Organism Page]]''' '''[[SEED_Viewer_Manual/KEGG|KEGG]]''' '''[[SEED_Viewer_Manual/HomologClusters|Homolog Clusters]]''' '''[[SEED_Viewer_Manual/CompareMetabolicReconstruction|Compare Metabolic Reconstruction]]''' '''[[SEED_Viewer_Manual/MultiGenomeCompare|Multi Genome Compare]]''' ca4aba5043efe6e69e9372111779c42c2f696a8a 2191 2189 2008-11-26T17:00:28Z DanielaBartels 10 /* Main pages of the SeedViewer */ wikitext text/x-wiki == Main pages of the SeedViewer == ''' [[SEED_Viewer_Manual|Home Page]] ''' ''' [[SEED_Viewer_Manual/Menu|Menu]] ''' ''' [[SEED_Viewer_Manual/SubsystemSelect|Subsystem Select]] ''' '''[[SEED_Viewer_Manual/Subsystems|Subsystems]]''' '''[[SEED_Viewer_Manual/FunctionaRole|Functional Role]]''' '''[[SEED_Viewer_Manual/FIGfamViewer|FIGfam Viewer]]''' '''[[SEED_Viewer_Manual/Annotation|Annotation]]''' '''[[SEED_Viewer_Manual/Evidence|Evidence]]''' '''[[SEED_Viewer_Manual/BLASTOrganism|BLAST against an organism]]''' '''[[SEED_Viewer_Manual/ShowSeqs|Sequence]]''' '''[[SEED_Viewer_Manual/GenomeBrowser|Browse Genome]]''' '''[[SEED_Viewer_Manual/OrganismSelect|Organism Select]]''' '''[[SEED_Viewer_Manual/OrganismPage|Organism Page]]''' '''[[SEED_Viewer_Manual/KEGG|KEGG]]''' '''[[SEED_Viewer_Manual/HomologClusters|Homolog Clusters]]''' '''[[SEED_Viewer_Manual/CompareMetabolicReconstruction|Compare Metabolic Reconstruction]]''' '''[[SEED_Viewer_Manual/MultiGenomeCompare|Multi Genome Compare]]''' '''[[SEED_Viewer_Manual/KEGG|KEGG]]''' 842a54f9bc85d8f622f5eed7135ebdd7101a8821 2192 2191 2008-11-26T17:00:43Z DanielaBartels 10 /* Main pages of the SeedViewer */ wikitext text/x-wiki == Main pages of the SeedViewer == ''' [[SEED_Viewer_Manual|Home Page]] ''' ''' [[SEED_Viewer_Manual/Menu|Menu]] ''' ''' [[SEED_Viewer_Manual/SubsystemSelect|Subsystem Select]] ''' '''[[SEED_Viewer_Manual/Subsystems|Subsystems]]''' '''[[SEED_Viewer_Manual/FunctionaRole|Functional Role]]''' '''[[SEED_Viewer_Manual/FIGfamViewer|FIGfam Viewer]]''' '''[[SEED_Viewer_Manual/Annotation|Annotation]]''' '''[[SEED_Viewer_Manual/Evidence|Evidence]]''' '''[[SEED_Viewer_Manual/BLASTOrganism|BLAST against an organism]]''' '''[[SEED_Viewer_Manual/ShowSeqs|Sequence]]''' '''[[SEED_Viewer_Manual/GenomeBrowser|Browse Genome]]''' '''[[SEED_Viewer_Manual/OrganismSelect|Organism Select]]''' '''[[SEED_Viewer_Manual/OrganismPage|Organism Page]]''' '''[[SEED_Viewer_Manual/KEGG|KEGG]]''' '''[[SEED_Viewer_Manual/HomologClusters|Homolog Clusters]]''' '''[[SEED_Viewer_Manual/CompareMetabolicReconstruction|Compare Metabolic Reconstruction]]''' '''[[SEED_Viewer_Manual/MultiGenomeCompare|Multi Genome Compare]]''' ca4aba5043efe6e69e9372111779c42c2f696a8a 2202 2192 2008-12-01T10:24:16Z DanielaBartels 10 /* Main pages of the SeedViewer */ wikitext text/x-wiki == Main pages of the SeedViewer == ''' [[SEED_Viewer_Manual|Home Page]] ''' ''' [[SEED_Viewer_Manual/Menu|Menu]] ''' ''' [[SEED_Viewer_Manual/SubsystemSelect|Subsystem Select]] ''' '''[[SEED_Viewer_Manual/Subsystems|Subsystems]]''' '''[[SEED_Viewer_Manual/FunctionalRole|Functional Role]]''' '''[[SEED_Viewer_Manual/FIGfamViewer|FIGfam Viewer]]''' '''[[SEED_Viewer_Manual/Annotation|Annotation]]''' '''[[SEED_Viewer_Manual/Evidence|Evidence]]''' '''[[SEED_Viewer_Manual/BLASTOrganism|BLAST against an organism]]''' '''[[SEED_Viewer_Manual/ShowSeqs|Sequence]]''' '''[[SEED_Viewer_Manual/GenomeBrowser|Browse Genome]]''' '''[[SEED_Viewer_Manual/OrganismSelect|Organism Select]]''' '''[[SEED_Viewer_Manual/OrganismPage|Organism Page]]''' '''[[SEED_Viewer_Manual/KEGG|KEGG]]''' '''[[SEED_Viewer_Manual/HomologClusters|Homolog Clusters]]''' '''[[SEED_Viewer_Manual/CompareMetabolicReconstruction|Compare Metabolic Reconstruction]]''' '''[[SEED_Viewer_Manual/MultiGenomeCompare|Multi Genome Compare]]''' 1437f9f4927e27b30229ad3098c3ed59dfc34e86 2203 2202 2008-12-01T10:24:35Z DanielaBartels 10 /* Main pages of the SeedViewer */ wikitext text/x-wiki == Main pages of the SeedViewer == ''' [[SEED_Viewer_Manual|Home Page]] ''' ''' [[SEED_Viewer_Manual/Menu|Menu]] ''' ''' [[SEED_Viewer_Manual/SubsystemSelect|Subsystem Select]] ''' '''[[SEED_Viewer_Manual/Subsystems|Subsystems]]''' '''[[SEED_Viewer_Manual/FunctionalRoles|Functional Role]]''' '''[[SEED_Viewer_Manual/FIGfamViewer|FIGfam Viewer]]''' '''[[SEED_Viewer_Manual/Annotation|Annotation]]''' '''[[SEED_Viewer_Manual/Evidence|Evidence]]''' '''[[SEED_Viewer_Manual/BLASTOrganism|BLAST against an organism]]''' '''[[SEED_Viewer_Manual/ShowSeqs|Sequence]]''' '''[[SEED_Viewer_Manual/GenomeBrowser|Browse Genome]]''' '''[[SEED_Viewer_Manual/OrganismSelect|Organism Select]]''' '''[[SEED_Viewer_Manual/OrganismPage|Organism Page]]''' '''[[SEED_Viewer_Manual/KEGG|KEGG]]''' '''[[SEED_Viewer_Manual/HomologClusters|Homolog Clusters]]''' '''[[SEED_Viewer_Manual/CompareMetabolicReconstruction|Compare Metabolic Reconstruction]]''' '''[[SEED_Viewer_Manual/MultiGenomeCompare|Multi Genome Compare]]''' e47427b13de3e22411d4967d162087899012c0b8 2226 2203 2008-12-01T14:01:52Z DanielaBartels 10 /* Main pages of the SeedViewer */ wikitext text/x-wiki == Main pages of the SeedViewer == ''' [[SEED_Viewer_Manual|Home Page]] ''' ''' [[SEED_Viewer_Manual/Menu|Menu]] ''' ''' [[SEED_Viewer_Manual/SubsystemSelect|Subsystem Select]] ''' '''[[SEED_Viewer_Manual/Subsystems|Subsystems]]''' '''[[SEED_Viewer_Manual/FunctionalRoles|Functional Role]]''' '''[[SEED_Viewer_Manual/FIGfamViewer|FIGfam Viewer]]''' '''[[SEED_Viewer_Manual/Annotation|Annotation]]''' '''[[SEED_Viewer_Manual/Evidence|Evidence]]''' '''[[SEED_Viewer_Manual/BLASTOrganism|BLAST against an organism]]''' '''[[SEED_Viewer_Manual/ShowSeqs|Sequence]]''' '''[[SEED_Viewer_Manual/GenomeBrowser|Browse Genome]]''' '''[[SEED_Viewer_Manual/OrganismSelect|Organism Select]]''' '''[[SEED_Viewer_Manual/OrganismPage|Organism Page]]''' '''[[SEED_Viewer_Manual/KEGG|KEGG]]''' '''[[SEED_Viewer_Manual/HomologClusters|Homolog Clusters]]''' '''[[SEED_Viewer_Manual/CompareMetabolicReconstruction|Compare Metabolic Reconstruction]]''' '''[[SEED_Viewer_Manual/MultiGenomeCompare|Multi Genome Compare]]''' '''[[SEED_Viewer_Manual/BLASTDotPlot|BLAST Dot Plot]]''' 10e011ae0ae87925bedfbc950a38a72b3f8eeb7d 0 1542 2184 2008-11-26T16:23:15Z DanielaBartels 10 wikitext text/x-wiki == Download Organism == [[Image:ExportOrganism.png]] ac1ec608bbf9ccf40e180dd588f4cc7af2e46c44 2186 2184 2008-11-26T16:48:00Z DanielaBartels 10 /* Download Organism */ wikitext text/x-wiki == Download Organism == This page offers you to download a variaty of different information and formats of data for an organism. If you want to access other information than accessible on this page you can go to out ftp site linked on the page. All features of the genome in protein FASTA format can be downloaded using the '''FASTA''' link. Right-click the link and [[Image:ExportOrganism.png]] b4fd1666f8caeba4c827a2583ac94db209f03f39 2188 2186 2008-11-26T16:56:47Z DanielaBartels 10 /* Download Organism */ wikitext text/x-wiki == Download Organism == This page offers you to download a variaty of different information and formats of data for an organism. If you want to access other information than accessible on this page you can go to out ftp site linked on the page. All features of the genome in protein FASTA format can be downloaded using the '''FASTA''' link. Right-click the link and save the content to a file to get a fasta file. To get a tab-separated table of all features and the information visible in the table below, click the '''Tabular''' link and save it to a file. If you only want to download features with certain characteristics, you can filter the [[WebComponents/Table|table]] on the page and click the '''export''' button. This will let you save a file with only the filtered features. [[Image:ExportOrganism.png]] 938c6623266e443a958174a513d787692cce3567 6 1543 2185 2008-11-26T16:23:59Z DanielaBartels 10 wikitext text/x-wiki da39a3ee5e6b4b0d3255bfef95601890afd80709 0 1517 2187 2127 2008-11-26T16:55:35Z TobiasPaczian 17 /* Subsystems */ wikitext text/x-wiki == Subsystems == A [[Glossary#Subsystem|subsystem]] is a collection of [[Glossary#Functional role|functional roles]] that are associated to each other in a system. Such a system can be a metabolic pathway, a component of a cell like a secretion system and others. The subsystem page in the SeedViewer is divided into different parts via a [[WebComponents/Tabview|TabView]]. The TabView can consist of 3-5 tabs. The first tab shows a '''Diagram''' of the subsystem, the second tab displays a [[WebComponents/Table|table]] with the '''Functional Roles''' present in the subsystem. The '''Spreadsheet''' relating the functional roles in the subsystem to features in genomes can be found in the third tab. The fourth and fifth tab show a description and additional notes to a subsystem. They only appear if a subsystem has a description / notes. === Diagram === The subsystem diagram shows the connections between the functional roles in a subsystem. The boxes represent the functional roles via their abbreviations. The circles are connecting intermediates, that are described in the table which is part of the diagram. The functional roles in the diagram can be colored according to their presence in a genome. Click the button '''Color Diagram''' to get a combo box with all genomes in the subsystem. Select your genome of interest and press '''do coloring'''. The boxes for the functional roles defined for that genome will now be colored in green. [[Image:SubsystemDiagram.png]] === Functional Roles === This [[WebComponents/Table|table]] lists all functional roles present in the subsystem. The first column shows '''Group Aliases''' for the functional role. Functional roles can be aggregated in groups (subsets). Subset names that start with a '*' contain alternative ways to implement a function. The abbreviation ('''Abbrev.''') for a functional role must be unique for the functional roles in the subsystem. They are used in different displays like the Diagram or the Speadsheet. The third column lists the full name of the functional role. EC-Numbers are often part of the functional role (for enzymes), and are stated in parentheses after the name of the functional role. The following two columns deal with reactions a functional role is connected to. Clicking on the link opens a new window showing the KEGG reaction. Next to annotator-curated KEGG reactions, we show the KEGG reactions of the curation effort of the [[SEED_People#Hope College|Hope College]] team that collaborates with the SEED. GeneOntology (GO) links are displayed in the next column. The links point to the GO-number in GeneOntology's Amigo-Tool. The last column can contain literature (PubMed IDs) that describes the functional role in detail. If present, you will find a link to PubMed in this column. [[Image:SubsystemFRs.png]] === Spreadsheet === The subsystem spreadsheet displays the features that are assigned with the functional roles in all organisms that are part of the subsystem. The organisms are displayed in the first column. The links lead to the [[SEED_Viewer_Manual/OrganismPage|Organism Page]]. The column header includes a filter option for the organism, doing an infix search on the organism name. The '''Domain''' (Bacterial, Archaeal or Eukaryote) of the organism is shown in the second column. For each organism in the spreadsheet, a '''Variant Code''' is assigned. Usually, there is more than one way to fulfill a subsystem. Metabolic pathways can have alternatives, or parts of the pathway may be present or absent in an organism. [[[Glossary/Variant Code|Variant Codes]] are assigned to the organism to express this behavior. There are two special Variant Codes: '''0''' and '''-1'''. The Variant Code '''-1''' means that the organism has no active variant in this subsystem, meaning it does not implement the subsystem. '''0''' means that the curator has not yet assigned a variant to the genome. Due to the flow of newly sequenced genomes into the SEED, this variant code may show up sometimes. The next column is used to filter active or not active variants. If you want to see only the active ones (default), print '''yes''' into the filter in the column header. For seeing only the not active ones, print '''no'''. No input in this field will show all variants. All following columns in the table show the features in the organisms that are assigned with functional roles. The column headers display the abbreviations of the functional roles (see Functional Roles Table) Hovering over a column header will show a tooltip with the full name of the role. The feature entries in the cells for the functional roles are linked to the [[SEED_Viewer_Manual/Annotation|Annotation Page]] for that feature. There can be multiple features in a cell, as some functions are implemented by more that one feature in an organism. The control table on top of the spreadsheet table lets you change the display in the table: Functional Roles that belong to a subset starting with a '*', meaning they are alternatives for a function, are collapsed in the spreadsheet by default. If you want to expand the subsets, you can do so by checking '''expanded''' in the '''Subsets''' column. The feature entries in the spreadsheet can be colored according to different metaphors using the second column ('''Coloring''') of the table. By default, the features are colored '''by cluster'''. In this case, it is computed which features are close by on the genomic sequence, meaning they cluster. Each computed cluster gets its own color. These colors only have a meaning per genome, meaning that a yellow cluster in one genome has no connection to a yellow cluster in the next genome. Another way to cluster the features are different kinds of attributes. Check the radio box for '''by attribute''' and choose an attribute in the drop down menu. Press '''update''' to change the display. [[Image:SubsystemSpreadsheet.png]] === Description === The description of a subsystem gives an overview of the functional roles and their connections in the subsystem. It can give some background information about the system, what organisms it is usually found in and other facts that are of interest. === Additional Notes === As the description already gives an overview over the subsystem, additional notes can be found here. The notes usually refer to specific properties of some organisms or organism groups, genes that are missing but should be there and other details that might be useful for the interested user. 98a141dcdc252646a4349ac7e8d156caeb933b58 0 1525 2190 2147 2008-11-26T17:00:09Z TobiasPaczian 17 /* Export */ wikitext text/x-wiki == Table == The Table component has a large number of functionalities that can be used to access data that can be displayed in tabular form. Features of the table component are '''Browsing''', '''Sorting''', '''Filtering''' and '''Export'''. Most of these functions of the table are implemented by JavaScript functions. That means, it does not lead to a reload of the page. The page ''knows'' all the information, but only part of it is displayed. The display is then manipulated using JavaScript functions. A table consists of a header row (here in dark blue) and the rows that contain the data. In some cases the header row can be supplied with a supercolumn to group columns. The header cells contain the functionality to sort and filter the row data, as described below. The rows are colored in two different colors for better visibility (here white and light grey background). If you hover over a row, it will be highlighted in dark grey. [[Image:Table1.png]] === Browsing === The number of rows you want your table to display at once can be changed using the text box '''display ___ items per page'''. Just press return after changing the number to change the display of your table. To browse through the table you can click the links '''<<first''', '''<<prev''', '''next>>''' and '''last>>'''. The links only appear if there is e.g. a next page. The text in the middle of the links will tell you which items are currently displayed. [[Image:TableBrowse.png]] === Sorting === You can sort the contents of the table by each column using the little arrows next to the column header. The sorting is done using JavaScript, meaning that it does not reload the page. [[Image:TableSort.png]] === Filtering === Different kinds of filters can be applied to the table data. The table always uses all filters for all columns at once. This means that if you may want to check if other filters are active, if the result of filtering a column is not what you expect. Often, a '''clear all filters''' button is made available on top of the page. One filter is simply a text field that does an infix search (meaning that if the word you type in the text field is part of a word in the cells of a cell in the respective column, the row will be visible). [[Image:TableFilter1.png]] The combo box filter is usually used if only a small number of different values are used in a column. These values appear in the combo box if you click the arrow next to the textfield. Choose one and the table will filter automatically. [[Image:TableFilter2.png]] If a column consists of numbers, you will often get a filter using operators ('''>''', '''<''', '''=''' and others). You can choose one of these operators, and put a number into the text field below the operator to filter the table. [[Image:TableFilter3.png]] === Export === For most tables, you will find an '''export''' button on the page. This will let you download the data of the table in '''.tsv''' format. This tab-separated text can be opened with many editors and spreadsheet tools (i.e. Microsoft Excel). 42af8121c9d2da9ad72012cf9837cd74d5273ed3 0 1544 2193 2008-11-26T17:07:41Z DanielaBartels 10 wikitext text/x-wiki == Functional Role Page == 03991a8ebbc11056280afc080271e02adb41a036 2194 2193 2008-12-01T09:40:42Z DanielaBartels 10 wikitext text/x-wiki == Functional Role Page == [[Image:FunctionalRole1.png]] [[Image:FunctionalRole2.png]] c801e79c6545924f3b8b97a20ccc9c279acb49e4 2197 2194 2008-12-01T10:12:56Z DanielaBartels 10 /* Functional Role Page */ wikitext text/x-wiki == Functional Role Page == This page displays a functional role in context of a subsystem. The left part of the top table shows the '''Functional Role''' and the context '''Subsystem'''. If present, an '''EC-number''' or '''GO-number''' are listed. '''Reactions''' are [http://www.genome.ad.jp|KEGG] reactions that are bound to the EC-number. [[Image:FunctionalRole1.png]] [[Image:FunctionalRole2.png]] a0b17c61c2ffbfd256cfaccce1903231e9efca0d 2198 2197 2008-12-01T10:17:45Z DanielaBartels 10 /* Functional Role Page */ wikitext text/x-wiki == Functional Role Page == This page displays a functional role in context of a subsystem. The left part of the top table shows the '''Functional Role''' and the context '''Subsystem'''. If present, an '''EC-number''' or '''GO-number''' are listed. '''Reactions''' are [http://www.genome.ad.jp | KEGG] reactions that are bound to the EC-number. [[Image:FunctionalRole1.png]] [[Image:FunctionalRole2.png]] a44a00d811ae4a529856742f59707af08505566c 2199 2198 2008-12-01T10:18:29Z DanielaBartels 10 /* Functional Role Page */ wikitext text/x-wiki == Functional Role Page == This page displays a functional role in context of a subsystem. The left part of the top table shows the '''Functional Role''' and the context '''Subsystem'''. If present, an '''EC-number''' or '''GO-number''' are listed. '''Reactions''' are [http://www.genome.ad.jp|KEGG] reactions that are bound to the EC-number. [[Image:FunctionalRole1.png]] [[Image:FunctionalRole2.png]] a0b17c61c2ffbfd256cfaccce1903231e9efca0d 2200 2199 2008-12-01T10:23:04Z DanielaBartels 10 /* Functional Role Page */ wikitext text/x-wiki == Functional Role Page == This page displays a functional role in context of a subsystem. The left part of the top table shows the '''Functional Role''' and the context '''Subsystem'''. If present, an '''EC-number''' or '''GO-number''' are listed. '''Reactions''' are [http://www.genome.ad.jp KEGG] reactions that are bound to the EC-number. [[Image:FunctionalRole1.png]] [[Image:FunctionalRole2.png]] 94daa7c4a6e2986d9193d3826dc400615fff2aab 2201 2200 2008-12-01T10:23:43Z DanielaBartels 10 /* Functional Role Page */ wikitext text/x-wiki == Functional Role Page == This page displays a functional role in context of a subsystem. The left part of the top table shows the '''Functional Role''' and the context '''Subsystem'''. If present, an '''EC-number''' or '''GO-number''' are listed. '''Reactions''' are [http://www.genome.ad.jp/kegg/ KEGG] reactions that are bound to the EC-number. [[Image:FunctionalRole1.png]] [[Image:FunctionalRole2.png]] 68eae1cc54fd75a08c117b976e5f0cad9f30103b 2204 2201 2008-12-01T10:27:46Z DanielaBartels 10 /* Functional Role Page */ wikitext text/x-wiki == Functional Role Page == This page displays a functional role in context of a subsystem. The left part of the top table shows the '''Functional Role''' and the context '''Subsystem'''. If present, an '''EC-number''' or '''GO-number''' are listed. The EC-number links to the [http://www.genome.ad.jp/kegg/ KEGG] enzyme page for the enzyme. '''Reactions''' are [http://www.genome.ad.jp/kegg/ KEGG] reactions that are bound to the EC-number. [[Image:FunctionalRole1.png]] [[Image:FunctionalRole2.png]] 827037be29a438055e288c3d3b9390f8669520b5 2205 2204 2008-12-01T10:35:28Z DanielaBartels 10 /* Functional Role Page */ wikitext text/x-wiki == Functional Role Page == This page displays a functional role in context of a subsystem. The left part of the top table shows the '''Functional Role''' and the context '''Subsystem'''. If present, an '''EC-number''' or '''GO-number''' and '''Reactions''' are listed. The EC-number links to the [http://www.genome.ad.jp/kegg/ KEGG] enzyme page for the enzyme. GO-numbers are [www.geneontology.org GeneOntology classifications for a role. The link leads to the GO-Viewer [http://www.amigo.org AmiGo]. Reactions are [http://www.genome.ad.jp/kegg/ KEGG] reactions that are bound to the EC-number. [[Image:FunctionalRole1.png]] [[Image:FunctionalRole2.png]] bdfd2cec7b3d4fcb4a4fa7e1c71a6ba7faca237e 2206 2205 2008-12-01T10:41:02Z DanielaBartels 10 /* Functional Role Page */ wikitext text/x-wiki == Functional Role Page == This page displays a functional role in context of a subsystem. The left part of the top table shows the '''Functional Role''' and the context '''Subsystem'''. If present, an '''EC-number''' or '''GO-number''' and '''Reactions''' are listed. The EC-number links to the [http://www.genome.ad.jp/kegg/ KEGG] enzyme page for the enzyme. GO-numbers are [http://www.geneontology.org GeneOntology] classifications for a role. The link leads to the GO-Viewer [http://www.amigo.org AmiGo]. Reactions are [http://www.genome.ad.jp/kegg/ KEGG] reactions that are bound to the EC-number. [[Image:FunctionalRole1.png]] [[Image:FunctionalRole2.png]] 01220a79dc357830842306fce85b1b2b50c5a42d 2207 2206 2008-12-01T10:43:18Z DanielaBartels 10 /* Functional Role Page */ wikitext text/x-wiki == Functional Role Page == This page displays a functional role in context of a subsystem. The left part of the top table shows the '''Functional Role''' and the context '''Subsystem'''. If present, an '''EC-number''' or '''GO-number''' and '''Reactions''' are listed. The EC-number links to the [http://www.genome.ad.jp/kegg/ KEGG] enzyme page for the enzyme. GO-numbers are [http://www.geneontology.org GeneOntology] classifications for a role. The link leads to the GO-Viewer [http://amigo.geneontology.org/cgi-bin/amigo/search.cgi?session_id=9978amigo1228128113 AmiGo]. Reactions are [http://www.genome.ad.jp/kegg/ KEGG] reactions that are bound to the EC-number. [[Image:FunctionalRole1.png]] [[Image:FunctionalRole2.png]] 882e2267e74a01d9bd80298ca5c25633581e5a56 2208 2207 2008-12-01T10:44:03Z DanielaBartels 10 /* Functional Role Page */ wikitext text/x-wiki == Functional Role Page == This page displays a functional role in context of a subsystem. The left part of the top table shows the '''Functional Role''' and the context '''Subsystem'''. If present, an '''EC-number''' or '''GO-number''' and '''Reactions''' are listed. The EC-number links to the [http://www.genome.ad.jp/kegg/ KEGG] enzyme page for the enzyme. GO-numbers are [http://www.geneontology.org GeneOntology] classifications for a role. The link leads to the GO-Viewer [http://amigo.geneontology.org/cgi-bin/amigo/search.cgi AmiGo]. Reactions are [http://www.genome.ad.jp/kegg/ KEGG] reactions that are bound to the EC-number. [[Image:FunctionalRole1.png]] [[Image:FunctionalRole2.png]] 97e15a05d6feeee062c6279c9a11630840caa33f 2209 2208 2008-12-01T10:50:56Z DanielaBartels 10 /* Functional Role Page */ wikitext text/x-wiki == Functional Role Page == This page displays a functional role in context of a subsystem. The left part of the top table shows the '''Functional Role''' and the context '''Subsystem'''. If present, an '''EC-number''' or '''GO-number''' and '''Reactions''' are listed. The EC-number links to the [http://www.genome.ad.jp/kegg/ KEGG] enzyme page for the enzyme. GO-numbers are [http://www.geneontology.org GeneOntology] classifications for a role. The link leads to the GO-Viewer [http://amigo.geneontology.org/cgi-bin/amigo/search.cgi AmiGo]. Reactions are [http://www.genome.ad.jp/kegg/ KEGG] reactions that are bound to the EC-number. The left part of the table gives an overview of the assignments of the functional role to SEED features. '''Number of Occurrences''' is the total number of features that are assigned with the role. '''Number of Organisms''' is the number of different organisms that contain at least one feature assigned with the role. Then they are devided by domains of the organisms (Archaea, Bacteria, Eukaryota or Virus). [[Image:FunctionalRole1.png]] [[Image:FunctionalRole2.png]] 12354a5a28aaab1b9f4e0684ff38d034fab1f9c7 2210 2209 2008-12-01T11:04:16Z DanielaBartels 10 /* Functional Role Page */ wikitext text/x-wiki == Functional Role Page == This page displays a functional role in context of a subsystem. The left part of the top table shows the '''Functional Role''' and the context '''Subsystem'''. If present, an '''EC-number''' or '''GO-number''' and '''Reactions''' are listed. The EC-number links to the [http://www.genome.ad.jp/kegg/ KEGG] enzyme page for the enzyme. GO-numbers are [http://www.geneontology.org GeneOntology] classifications for a role. The link leads to the GO-Viewer [http://amigo.geneontology.org/cgi-bin/amigo/search.cgi AmiGo]. Reactions are [http://www.genome.ad.jp/kegg/ KEGG] reactions that are bound to the EC-number. The left part of the table gives an overview of the assignments of the functional role to SEED features. '''Number of Occurrences''' is the total number of features that are assigned with the role. '''Number of Organisms''' is the number of different organisms that contain at least one feature assigned with the role. Then they are devided by domains of the organisms (Archaea, Bacteria, Eukaryota or Virus). [[Image:FunctionalRole1.png]] The table below lists all features that are assigned with the functional role. The feature ID links to the [[SEED_Viewer_Manual/Annotation|Annotation page]] for the feature. The organism link in the second column of the table points to the [[SEED_Viewer_Manual/OrganismPage|Organism Page]] for that organism. The domain of the organism is depicted in the third column. [[Image:FunctionalRole2.png]] 579e2d8793a0cf803ac62dd9c5c399882c404e39 2211 2210 2008-12-01T11:09:25Z DanielaBartels 10 /* Functional Role Page */ wikitext text/x-wiki == Functional Role Page == This page displays a functional role in context of a subsystem. The left part of the top table shows the '''Functional Role''' and the context '''Subsystem'''. If present, an '''EC-number''' or '''GO-number''' and '''Reactions''' are listed. The EC-number links to the [http://www.genome.ad.jp/kegg/ KEGG] enzyme page for the enzyme. GO-numbers are [http://www.geneontology.org GeneOntology] classifications for a role. The link leads to the GO-Viewer [http://amigo.geneontology.org/cgi-bin/amigo/search.cgi AmiGo]. Reactions are [http://www.genome.ad.jp/kegg/ KEGG] reactions that are bound to the EC-number. The left part of the table gives an overview of the assignments of the functional role to SEED features. '''Number of Occurrences''' is the total number of features that are assigned with the role. '''Number of Organisms''' is the number of different organisms that contain at least one feature assigned with the role. Then they are devided by domains of the organisms (Archaea, Bacteria, Eukaryota or Virus). [[Image:FunctionalRole1.png]] The table below lists all features that are assigned with the functional role. The feature ID links to the [[SEED_Viewer_Manual/Annotation|Annotation page]] for the feature. The organism link in the second column of the table points to the [[SEED_Viewer_Manual/OrganismPage|Organism Page]] for that organism. The domain of the organism is depicted in the third column. You can download the table in ''comma-separated format'' using the '''export table''' button. To gain access the sequences of the listed features, press the '''show sequences''' button that opens the [[SEED_Viewer_Manual/ShowSeqs|Sequence''' page. [[Image:FunctionalRole2.png]] 21d1bd7f1fc2e0834a489b5daef99ba7cd3fd67f 2212 2211 2008-12-01T11:09:46Z DanielaBartels 10 /* Functional Role Page */ wikitext text/x-wiki == Functional Role Page == This page displays a functional role in context of a subsystem. The left part of the top table shows the '''Functional Role''' and the context '''Subsystem'''. If present, an '''EC-number''' or '''GO-number''' and '''Reactions''' are listed. The EC-number links to the [http://www.genome.ad.jp/kegg/ KEGG] enzyme page for the enzyme. GO-numbers are [http://www.geneontology.org GeneOntology] classifications for a role. The link leads to the GO-Viewer [http://amigo.geneontology.org/cgi-bin/amigo/search.cgi AmiGo]. Reactions are [http://www.genome.ad.jp/kegg/ KEGG] reactions that are bound to the EC-number. The left part of the table gives an overview of the assignments of the functional role to SEED features. '''Number of Occurrences''' is the total number of features that are assigned with the role. '''Number of Organisms''' is the number of different organisms that contain at least one feature assigned with the role. Then they are devided by domains of the organisms (Archaea, Bacteria, Eukaryota or Virus). [[Image:FunctionalRole1.png]] The table below lists all features that are assigned with the functional role. The feature ID links to the [[SEED_Viewer_Manual/Annotation|Annotation page]] for the feature. The organism link in the second column of the table points to the [[SEED_Viewer_Manual/OrganismPage|Organism Page]] for that organism. The domain of the organism is depicted in the third column. You can download the table in ''comma-separated format'' using the '''export table''' button. To gain access the sequences of the listed features, press the '''show sequences''' button that opens the [[SEED_Viewer_Manual/ShowSeqs|Sequence]] page. [[Image:FunctionalRole2.png]] 10e1106fdc76531390e32bbd095fa6856e0f5058 6 1545 2195 2008-12-01T09:42:24Z DanielaBartels 10 wikitext text/x-wiki da39a3ee5e6b4b0d3255bfef95601890afd80709 6 1546 2196 2008-12-01T09:43:20Z DanielaBartels 10 wikitext text/x-wiki da39a3ee5e6b4b0d3255bfef95601890afd80709 0 1547 2213 2008-12-01T11:34:42Z DanielaBartels 10 wikitext text/x-wiki == Show Sequences == [[Image:ShowSeqs.png]] 89e347e8fc319bf9f3563bb3be54b08fc1a46cd3 2215 2213 2008-12-01T11:55:55Z DanielaBartels 10 /* Show Sequences */ wikitext text/x-wiki == Display fasta sequences == This page shows sequences of given features. Usually, you enter this page from a page where you have selected a number of sequences. You can download or display the sequences using the '''Download Sequences''' or '''Show Fasta''' buttons. The header of the fasta sequences is in the format ''>feature_id \[Organism id\] \[annotation\]. You can choose between three options for the sequences: 1) '''DNA Sequence''' Provides you with the DNA sequence in fasta format. 2) '''DNA Sequence with flanking''' Also DNA sequence, but it adds a number of bases upstream and downstream to the feature. The sequence of the feature will then appear in upper-case letters, while the flanking sequences will be lower-case. 3) '''Protein Sequence''' The protein sequence (translated DNA). [[Image:ShowSeqs.png]] 05ae4c82c0d3b29e84eb95cc76b9d00a0e950ec1 2216 2215 2008-12-01T11:56:34Z DanielaBartels 10 /* Display fasta sequences */ wikitext text/x-wiki == Display fasta sequences == This page shows sequences of given features. Usually, you enter this page from a page where you have selected a number of sequences. You can download or display the sequences using the '''Download Sequences''' or '''Show Fasta''' buttons. The header of the fasta sequences is in the format ''>feature_id [Organism id] [annotation]''. You can choose between three options for the sequences: 1) '''DNA Sequence''' Provides you with the DNA sequence in fasta format. 2) '''DNA Sequence with flanking''' Also DNA sequence, but it adds a number of bases upstream and downstream to the feature. The sequence of the feature will then appear in upper-case letters, while the flanking sequences will be lower-case. 3) '''Protein Sequence''' The protein sequence (translated DNA). [[Image:ShowSeqs.png]] 1bdcc1b99a7eeb7621a020e0650cf1a75108fa69 2217 2216 2008-12-01T11:57:01Z DanielaBartels 10 /* Display fasta sequences */ wikitext text/x-wiki == Display fasta sequences == This page shows sequences of given features. Usually, you enter this page from a page where you have selected a number of sequences. You can download or display the sequences using the '''Download Sequences''' or '''Show Fasta''' buttons. The header of the fasta sequences is in the format ''>feature_id [Organism id] [annotation]''. You can choose between three options for the sequences: 1) '''DNA Sequence''' Provides you with the DNA sequence in fasta format. 2) '''DNA Sequence with flanking''' Also DNA sequence, but it adds a number of bases upstream and downstream to the feature. The sequence of the feature will then appear in upper-case letters, while the flanking sequences will be lower-case. 3) '''Protein Sequence''' The protein sequence (translated DNA). [[Image:ShowSeqs.png]] 166601068aaa7304c0923bdd4621aac3ac153e29 6 1548 2214 2008-12-01T11:35:00Z DanielaBartels 10 wikitext text/x-wiki da39a3ee5e6b4b0d3255bfef95601890afd80709 0 1549 2218 2008-12-01T12:10:33Z DanielaBartels 10 wikitext text/x-wiki == Multi Genome Compare == This page provides a way to compare a chosen organism against on or many others on the basis of the feature sequences (protein). 59895d4538396ea11011a19e7e7032b0775b4df1 2219 2218 2008-12-01T13:22:41Z DanielaBartels 10 /* Multi Genome Compare */ wikitext text/x-wiki == Multi Genome Compare == This page provides a way to compare a chosen organism against on or many others on the basis of the feature sequences (protein). [[Image:MCGResult.png]] 049457749fcd4c88a14789245328f943552cfe3c 2221 2219 2008-12-01T13:25:28Z DanielaBartels 10 /* Multi Genome Compare */ wikitext text/x-wiki == Multi Genome Compare == This page provides a way to compare a chosen organism against on or many others on the basis of the feature sequences (protein). [[Image:MCGResult.png]] [[Image:MCGResult2.png]] 9a21499d9d3ffc2f6978c959cc0b1a73d553a5be 2223 2221 2008-12-01T13:39:31Z DanielaBartels 10 /* Multi Genome Compare */ wikitext text/x-wiki == Multi Genome Compare == This page provides a way to compare a chosen organism against on or many others on the basis of the feature sequences (protein). [[Image:MCGStart.png]] [[Image:MCGResult.png]] [[Image:MCGResult2.png]] 8c55525c70dd8ccb8a77ae2588433d5e86882384 2225 2223 2008-12-01T13:59:59Z DanielaBartels 10 /* Multi Genome Compare */ wikitext text/x-wiki == Multi Genome Compare == This page provides a way to compare a chosen organism against on or many others on the basis of the feature sequences (protein). === Start the computation === To start a Multi Genome Comparison, you have to fulfill three steps: 1) '''Select Reference Genome''' The reference genome is used as a basis for the comparison. All selected genomes (step 2) will be projected on this one. Click [[SEED_Viewer_Manual/OrganismSelect|here]] to see how to select an organism. 2) '''Select Comparison Organisms''' You can select maximal four organisms to project on the reference genome. 3) '''Compute''' Press '''compute''' to start the computation. This may take while, as the system computes a bidirectional BLAST comparison of each genome to the reference genome. === Result === At the top of the result page you will see a list of the genomes involved in the comparison again. After each comparison genome, there is a button '''BlastDotPlot''' that leads to a [[SEED_Viewer_Manual/BLASTDotPlot|dot plot of the BLAST comparison]] between the comparison organism and the reference genome. [[Image:MCGResult.png]] [[Image:MCGResult2.png]] 3ed71a2c206b98c7f04e592613eedcf3bd5b8e3e 2227 2225 2008-12-01T14:17:50Z DanielaBartels 10 /* Result */ wikitext text/x-wiki == Multi Genome Compare == This page provides a way to compare a chosen organism against on or many others on the basis of the feature sequences (protein). === Start the computation === To start a Multi Genome Comparison, you have to fulfill three steps: 1) '''Select Reference Genome''' The reference genome is used as a basis for the comparison. All selected genomes (step 2) will be projected on this one. Click [[SEED_Viewer_Manual/OrganismSelect|here]] to see how to select an organism. 2) '''Select Comparison Organisms''' You can select maximal four organisms to project on the reference genome. 3) '''Compute''' Press '''compute''' to start the computation. This may take while, as the system computes a bidirectional BLAST comparison of each genome to the reference genome. === Result === At the top of the result page you will see a list of the genomes involved in the comparison again. After each comparison genome, there is a button '''BlastDotPlot''' that leads to a [[SEED_Viewer_Manual/BLASTDotPlot|dot plot of the BLAST comparison]] between the comparison organism and the reference genome. [[Image:MCGResulta.png]] [[Image:MCGResultb.png]] [[Image:MCGResultc.png]] [[Image:MCGResult2.png]] 91d8b5950dc1f4d71b395c6d34615ffb9d72b6cf 6 1550 2220 2008-12-01T13:23:10Z DanielaBartels 10 wikitext text/x-wiki da39a3ee5e6b4b0d3255bfef95601890afd80709 6 1551 2222 2008-12-01T13:25:55Z DanielaBartels 10 wikitext text/x-wiki da39a3ee5e6b4b0d3255bfef95601890afd80709 6 1552 2224 2008-12-01T13:40:47Z DanielaBartels 10 wikitext text/x-wiki da39a3ee5e6b4b0d3255bfef95601890afd80709 6 1553 2228 2008-12-01T14:18:43Z DanielaBartels 10 wikitext text/x-wiki da39a3ee5e6b4b0d3255bfef95601890afd80709 6 1554 2229 2008-12-01T14:21:12Z DanielaBartels 10 wikitext text/x-wiki da39a3ee5e6b4b0d3255bfef95601890afd80709 6 1555 2230 2008-12-01T14:23:50Z DanielaBartels 10 wikitext text/x-wiki da39a3ee5e6b4b0d3255bfef95601890afd80709 0 1549 2231 2227 2008-12-01T14:26:28Z DanielaBartels 10 /* Result */ wikitext text/x-wiki == Multi Genome Compare == This page provides a way to compare a chosen organism against on or many others on the basis of the feature sequences (protein). === Start the computation === To start a Multi Genome Comparison, you have to fulfill three steps: 1) '''Select Reference Genome''' The reference genome is used as a basis for the comparison. All selected genomes (step 2) will be projected on this one. Click [[SEED_Viewer_Manual/OrganismSelect|here]] to see how to select an organism. 2) '''Select Comparison Organisms''' You can select maximal four organisms to project on the reference genome. 3) '''Compute''' Press '''compute''' to start the computation. This may take while, as the system computes a bidirectional BLAST comparison of each genome to the reference genome. === Result === At the top of the result page you will see a list of the genomes involved in the comparison again. After each comparison genome, there is a button '''BlastDotPlot''' that leads to a [[SEED_Viewer_Manual/BLASTDotPlot|dot plot of the BLAST comparison]] between the comparison organism and the reference genome. You can use the link '''change organism selection''' on top of the table if the selection does not fit. [[Image:MCGResulta.png]] [[Image:MCGResultb.png]] [[Image:MCGResultc.png]] [[Image:MCGResult2.png]] b88da745c55d1c0305b3d1f7a2b0cd7ba120a9ce 2232 2231 2008-12-01T14:50:33Z DanielaBartels 10 /* Result */ wikitext text/x-wiki == Multi Genome Compare == This page provides a way to compare a chosen organism against on or many others on the basis of the feature sequences (protein). === Start the computation === To start a Multi Genome Comparison, you have to fulfill three steps: 1) '''Select Reference Genome''' The reference genome is used as a basis for the comparison. All selected genomes (step 2) will be projected on this one. Click [[SEED_Viewer_Manual/OrganismSelect|here]] to see how to select an organism. 2) '''Select Comparison Organisms''' You can select maximal four organisms to project on the reference genome. 3) '''Compute''' Press '''compute''' to start the computation. This may take while, as the system computes a bidirectional BLAST comparison of each genome to the reference genome. === Result === At the top of the result page you will see a list of the genomes involved in the comparison again. After each comparison genome, there is a button '''BlastDotPlot''' that leads to a [[SEED_Viewer_Manual/BLASTDotPlot|dot plot of the BLAST comparison]] between the comparison organism and the reference genome. You can use the link '''change organism selection''' on top of the table if the selection does not fit. [[Image:MCGResulta.png]] The colored table below shows [[Image:MCGResultb.png]] [[Image:MCGResultc.png]] [[Image:MCGResult2.png]] 16cfe1a1399f2959b7d294b6d021012e827894f8 2233 2232 2008-12-01T16:15:52Z DanielaBartels 10 /* Result */ wikitext text/x-wiki == Multi Genome Compare == This page provides a way to compare a chosen organism against on or many others on the basis of the feature sequences (protein). === Start the computation === To start a Multi Genome Comparison, you have to fulfill three steps: 1) '''Select Reference Genome''' The reference genome is used as a basis for the comparison. All selected genomes (step 2) will be projected on this one. Click [[SEED_Viewer_Manual/OrganismSelect|here]] to see how to select an organism. 2) '''Select Comparison Organisms''' You can select maximal four organisms to project on the reference genome. 3) '''Compute''' Press '''compute''' to start the computation. This may take while, as the system computes a bidirectional BLAST comparison of each genome to the reference genome. === Result === At the top of the result page you will see a list of the genomes involved in the comparison again. After each comparison genome, there is a button '''BlastDotPlot''' that leads to a [[SEED_Viewer_Manual/BLASTDotPlot|dot plot of the BLAST comparison]] between the comparison organism and the reference genome. You can use the link '''change organism selection''' on top of the table if the selection does not fit. [[Image:MCGResulta.png]] The colored table below shows the outcome of the bidirectional BLAST comparisons between each comparison genome and the reference genome, projected on the reference genome. The colors in the table describe the '''Percent protein sequence identity''' of each gene to it's ortholog in the reference genome. [[Image:MCGResultb.png]] [[Image:MCGResultc.png]] [[Image:MCGResult2.png]] f1e3e070000ae1c83526049bf31bdcdb4325f151 2234 2233 2008-12-01T16:21:37Z DanielaBartels 10 /* Result */ wikitext text/x-wiki == Multi Genome Compare == This page provides a way to compare a chosen organism against on or many others on the basis of the feature sequences (protein). === Start the computation === To start a Multi Genome Comparison, you have to fulfill three steps: 1) '''Select Reference Genome''' The reference genome is used as a basis for the comparison. All selected genomes (step 2) will be projected on this one. Click [[SEED_Viewer_Manual/OrganismSelect|here]] to see how to select an organism. 2) '''Select Comparison Organisms''' You can select maximal four organisms to project on the reference genome. 3) '''Compute''' Press '''compute''' to start the computation. This may take while, as the system computes a bidirectional BLAST comparison of each genome to the reference genome. === Result === At the top of the result page you will see a list of the genomes involved in the comparison again. After each comparison genome, there is a button '''BlastDotPlot''' that leads to a [[SEED_Viewer_Manual/BLASTDotPlot|dot plot of the BLAST comparison]] between the comparison organism and the reference genome. You can use the link '''change organism selection''' on top of the table if the selection does not fit. [[Image:MCGResulta.png]] The colored table below shows the outcome of the bidirectional BLAST comparisons between each comparison genome and the reference genome, projected on the reference genome. The colors in the table describe the '''Percent protein sequence identity''' of each gene to it's ortholog in the reference genome. The legend on top of the table [[Image:MCGResultb.png]] [[Image:MCGResultc.png]] [[Image:MCGResult2.png]] d9724935d238df343a74c7fa26a654c8b954e01e 2235 2234 2008-12-01T16:23:06Z DanielaBartels 10 /* Result */ wikitext text/x-wiki == Multi Genome Compare == This page provides a way to compare a chosen organism against on or many others on the basis of the feature sequences (protein). === Start the computation === To start a Multi Genome Comparison, you have to fulfill three steps: 1) '''Select Reference Genome''' The reference genome is used as a basis for the comparison. All selected genomes (step 2) will be projected on this one. Click [[SEED_Viewer_Manual/OrganismSelect|here]] to see how to select an organism. 2) '''Select Comparison Organisms''' You can select maximal four organisms to project on the reference genome. 3) '''Compute''' Press '''compute''' to start the computation. This may take while, as the system computes a bidirectional BLAST comparison of each genome to the reference genome. === Result === At the top of the result page you will see a list of the genomes involved in the comparison again. After each comparison genome, there is a button '''BlastDotPlot''' that leads to a [[SEED_Viewer_Manual/BLASTDotPlot|dot plot of the BLAST comparison]] between the comparison organism and the reference genome. You can use the link '''change organism selection''' on top of the table if the selection does not fit. [[Image:MCGResulta.png]] The colored table below shows the outcome of the bidirectional BLAST comparisons between each comparison genome and the reference genome, projected on the reference genome. The colors in the table depicts the '''Percent protein sequence identity''' of each gene to it's ortholog in the reference genome. The legend on top of the table describes the coloring. [[Image:MCGResultb.png]] [[Image:MCGResultc.png]] [[Image:MCGResult2.png]] 5e6228093e9faa809265ac7a28c4c0ec99d826d6 2236 2235 2008-12-01T17:00:52Z DanielaBartels 10 /* Result */ wikitext text/x-wiki == Multi Genome Compare == This page provides a way to compare a chosen organism against on or many others on the basis of the feature sequences (protein). === Start the computation === To start a Multi Genome Comparison, you have to fulfill three steps: 1) '''Select Reference Genome''' The reference genome is used as a basis for the comparison. All selected genomes (step 2) will be projected on this one. Click [[SEED_Viewer_Manual/OrganismSelect|here]] to see how to select an organism. 2) '''Select Comparison Organisms''' You can select maximal four organisms to project on the reference genome. 3) '''Compute''' Press '''compute''' to start the computation. This may take while, as the system computes a bidirectional BLAST comparison of each genome to the reference genome. === Result === At the top of the result page you will see a list of the genomes involved in the comparison again. After each comparison genome, there is a button '''BlastDotPlot''' that leads to a [[SEED_Viewer_Manual/BLASTDotPlot|dot plot of the BLAST comparison]] between the comparison organism and the reference genome. You can use the link '''change organism selection''' on top of the table if the selection does not fit. [[Image:MCGResulta.png]] The colored table below shows the outcome of the bidirectional BLAST comparisons between each comparison genome and the reference genome, projected on the reference genome. The colors in the table depicts the '''Percent protein sequence identity''' of each gene to it's ortholog in the reference genome. The legend on top of the table describes the coloring. [[Image:MCGResultb.png]] The first three columns of the table refer to the chosen reference genome ('''Contig''', '''Gene''' and '''Length'''). The Gene ID links to the [[SEED_Viewer_Manual/Annotation|Annotation]] page for the feature. The best BLAST hit of the query feature in the comparison genome is shown in three columns in the table ('''Hit''', '''Contig''' and '''Gene'''). The color of the hit is determined by the percent identity of the query and the hit. No color means there is no hit. The '''Hit''' column contains a '-' (no hit), 'uni' or 'bi'. The '''bi''' stand for ''bidirectional best hit'', meaning that the reverse hit from the comparison genome to the reference genome is also the best hit (That's not always true if a genome contains many close paralogs for a feature). If it's not a bidirectional hit, it shows '''uni''' for uni-directional. [[Image:MCGResult2.png]] f4708035b82ecb618b5b899e5e7edd94951b1c88 2237 2236 2008-12-01T17:02:00Z DanielaBartels 10 /* Result */ wikitext text/x-wiki == Multi Genome Compare == This page provides a way to compare a chosen organism against on or many others on the basis of the feature sequences (protein). === Start the computation === To start a Multi Genome Comparison, you have to fulfill three steps: 1) '''Select Reference Genome''' The reference genome is used as a basis for the comparison. All selected genomes (step 2) will be projected on this one. Click [[SEED_Viewer_Manual/OrganismSelect|here]] to see how to select an organism. 2) '''Select Comparison Organisms''' You can select maximal four organisms to project on the reference genome. 3) '''Compute''' Press '''compute''' to start the computation. This may take while, as the system computes a bidirectional BLAST comparison of each genome to the reference genome. === Result === At the top of the result page you will see a list of the genomes involved in the comparison again. After each comparison genome, there is a button '''BlastDotPlot''' that leads to a [[SEED_Viewer_Manual/BLASTDotPlot|dot plot of the BLAST comparison]] between the comparison organism and the reference genome. You can use the link '''change organism selection''' on top of the table if the selection does not fit. [[Image:MCGResulta.png]] The colored table below shows the outcome of the bidirectional BLAST comparisons between each comparison genome and the reference genome, projected on the reference genome. The colors in the table depicts the '''Percent protein sequence identity''' of each gene to it's ortholog in the reference genome. The legend on top of the table describes the coloring. [[Image:MCGResultb.png]] The first three columns of the table refer to the chosen reference genome ('''Contig''', '''Gene''' and '''Length'''). The Gene ID links to the [[SEED_Viewer_Manual/Annotation|Annotation]] page for the feature. The best BLAST hit of the query feature in the comparison genome is shown in three columns in the table ('''Hit''', '''Contig''' and '''Gene'''). The color of the hit is determined by the percent identity of the query and the hit. No color means there is no hit. The '''Hit''' column contains a '-' (no hit), 'uni' or 'bi'. The '''bi''' stands for ''bidirectional best hit'', meaning that the reverse hit from the comparison genome to the reference genome is also the best hit (That's not always true if a genome contains many close paralogs for a feature). If it's not a bidirectional hit, it shows '''uni''' for uni-directional. [[Image:MCGResult2.png]] c3269edc20c146ce086af5fd9abd80d83536a44b 2238 2237 2008-12-01T17:02:38Z DanielaBartels 10 /* Result */ wikitext text/x-wiki == Multi Genome Compare == This page provides a way to compare a chosen organism against on or many others on the basis of the feature sequences (protein). === Start the computation === To start a Multi Genome Comparison, you have to fulfill three steps: 1) '''Select Reference Genome''' The reference genome is used as a basis for the comparison. All selected genomes (step 2) will be projected on this one. Click [[SEED_Viewer_Manual/OrganismSelect|here]] to see how to select an organism. 2) '''Select Comparison Organisms''' You can select maximal four organisms to project on the reference genome. 3) '''Compute''' Press '''compute''' to start the computation. This may take while, as the system computes a bidirectional BLAST comparison of each genome to the reference genome. === Result === At the top of the result page you will see a list of the genomes involved in the comparison again. After each comparison genome, there is a button '''BlastDotPlot''' that leads to a [[SEED_Viewer_Manual/BLASTDotPlot|dot plot of the BLAST comparison]] between the comparison organism and the reference genome. You can use the link '''change organism selection''' on top of the table if the selection does not fit. [[Image:MCGResulta.png]] The colored table below shows the outcome of the bidirectional BLAST comparisons between each comparison genome and the reference genome, projected on the reference genome. The colors in the table depicts the '''Percent protein sequence identity''' of each gene to it's ortholog in the reference genome. The legend on top of the table describes the coloring. [[Image:MCGResultb.png]] The first three columns of the table refer to the chosen reference genome ('''Contig''', '''Gene''' and '''Length'''). The Gene ID links to the [[SEED_Viewer_Manual/Annotation|Annotation]] page for the feature. The best BLAST hit of the query feature in the comparison genome is shown in three columns in the table ('''Hit''', '''Contig''' and '''Gene'''). The color of the hit is determined by the percent identity of the query and the hit. No color means there is no hit. The '''Hit''' column contains a '-' (no hit), 'uni' or 'bi'. The '''bi''' stands for ''bidirectional best hit'', meaning that the reverse hit from the comparison genome to the reference genome is also the best hit (That's not always true if a genome contains many close paralogs for a feature). If it's not a bidirectional hit, it shows '''uni''' for uni-directional. [[Image:MCGResultc.png]] [[Image:MCGResult2.png]] be346f9f68e929febdf7b563449a018eab4e43bf 2239 2238 2008-12-01T17:07:50Z DanielaBartels 10 /* Result */ wikitext text/x-wiki == Multi Genome Compare == This page provides a way to compare a chosen organism against on or many others on the basis of the feature sequences (protein). === Start the computation === To start a Multi Genome Comparison, you have to fulfill three steps: 1) '''Select Reference Genome''' The reference genome is used as a basis for the comparison. All selected genomes (step 2) will be projected on this one. Click [[SEED_Viewer_Manual/OrganismSelect|here]] to see how to select an organism. 2) '''Select Comparison Organisms''' You can select maximal four organisms to project on the reference genome. 3) '''Compute''' Press '''compute''' to start the computation. This may take while, as the system computes a bidirectional BLAST comparison of each genome to the reference genome. === Result === At the top of the result page you will see a list of the genomes involved in the comparison again. After each comparison genome, there is a button '''BlastDotPlot''' that leads to a [[SEED_Viewer_Manual/BLASTDotPlot|dot plot of the BLAST comparison]] between the comparison organism and the reference genome. You can use the link '''change organism selection''' on top of the table if the selection does not fit. [[Image:MCGResulta.png]] The colored [[WebComponents/Table|table]] below shows the outcome of the bidirectional BLAST comparisons between each comparison genome and the reference genome, projected on the reference genome. The colors in the table depicts the '''Percent protein sequence identity''' of each gene to it's ortholog in the reference genome. The legend on top of the table describes the coloring. [[Image:MCGResultb.png]] The first three columns of the table refer to the chosen reference genome ('''Contig''', '''Gene''' and '''Length'''). The Gene ID links to the [[SEED_Viewer_Manual/Annotation|Annotation]] page for the feature. The best BLAST hit of the query feature in the comparison genome is shown in three columns in the table ('''Hit''', '''Contig''' and '''Gene'''). The color of the hit is determined by the percent identity of the query and the hit. No color means there is no hit. The '''Hit''' column contains a '-' (no hit), 'uni' or 'bi'. The '''bi''' stands for ''bidirectional best hit'', meaning that the reverse hit from the comparison genome to the reference genome is also the best hit (That's not always true if a genome contains many close paralogs for a feature). If it's not a bidirectional hit, it shows '''uni''' for uni-directional. Each feature ID is again linked to the feature's [[SEED_Viewer_Manual/Annotation|Annotation Page]]. The contents of the table can be exported in ''tab-separated format'' using the '''export''' button on top of the table. The filters below the buttons refer to the percent identity for the features of each genome. You can choose to filter the table for the percent identity above or below a certain value for each genome, and also in combination. Use the button '''Clear all filters''' to reset the table. [[Image:MCGResultc.png]] [[Image:MCGResult2.png]] a67acd614f17f31677d579428811e5060b6bc01a 2240 2239 2008-12-01T17:13:41Z DanielaBartels 10 /* Result */ wikitext text/x-wiki == Multi Genome Compare == This page provides a way to compare a chosen organism against on or many others on the basis of the feature sequences (protein). === Start the computation === To start a Multi Genome Comparison, you have to fulfill three steps: 1) '''Select Reference Genome''' The reference genome is used as a basis for the comparison. All selected genomes (step 2) will be projected on this one. Click [[SEED_Viewer_Manual/OrganismSelect|here]] to see how to select an organism. 2) '''Select Comparison Organisms''' You can select maximal four organisms to project on the reference genome. 3) '''Compute''' Press '''compute''' to start the computation. This may take while, as the system computes a bidirectional BLAST comparison of each genome to the reference genome. === Result === At the top of the result page you will see a list of the genomes involved in the comparison again. After each comparison genome, there is a button '''BlastDotPlot''' that leads to a [[SEED_Viewer_Manual/BLASTDotPlot|dot plot of the BLAST comparison]] between the comparison organism and the reference genome. You can use the link '''change organism selection''' on top of the table if the selection does not fit. [[Image:MCGResulta.png]] The colored [[WebComponents/Table|table]] below shows the outcome of the bidirectional BLAST comparisons between each comparison genome and the reference genome, projected on the reference genome. The colors in the table depicts the '''Percent protein sequence identity''' of each gene to it's ortholog in the reference genome. The legend on top of the table describes the coloring. [[Image:MCGResultb.png]] The first three columns of the table refer to the chosen reference genome ('''Contig''', '''Gene''' and '''Length'''). The Gene ID links to the [[SEED_Viewer_Manual/Annotation|Annotation]] page for the feature. The best BLAST hit of the query feature in the comparison genome is shown in three columns in the table ('''Hit''', '''Contig''' and '''Gene'''). The color of the hit is determined by the percent identity of the query and the hit. No color means there is no hit. The '''Hit''' column contains a '-' (no hit), 'uni' or 'bi'. The '''bi''' stands for ''bidirectional best hit'', meaning that the reverse hit from the comparison genome to the reference genome is also the best hit (That's not always true if a genome contains many close paralogs for a feature). If it's not a bidirectional hit, it shows '''uni''' for uni-directional. Each feature ID is again linked to the feature's [[SEED_Viewer_Manual/Annotation|Annotation Page]]. Hovering over a cell in the table will show a tooltip with some information about the feature. The contents of the table can be exported in ''tab-separated format'' using the '''export''' button on top of the table. The filters below the buttons refer to the percent identity for the features of each genome. You can choose to filter the table for the percent identity above or below a certain value for each genome, and also in combination. Use the button '''clear all filters''' to reset the table. [[Image:MCGResultc.png]] The circular image right to the table is a whole genome view for the reference genome. Each circle represents a projection of a comparison genome to the reference genome. Keep in mind that the table as well as the graphic only shows features of the comparison genomes, that are hit by the reference genome. The order of the features is determined by the reference genome. If you click on a line in the graphics, the table will update and show the area that was clicked in the graphic. The red circle in the graphic determines the area the table currently displays. [[Image:MCGResult2.png]] 950062e786a2f4da01b0b46bb3b4e5a27813fe69 2241 2240 2008-12-02T09:21:31Z DanielaBartels 10 /* Result */ wikitext text/x-wiki == Multi Genome Compare == This page provides a way to compare a chosen organism against on or many others on the basis of the feature sequences (protein). === Start the computation === To start a Multi Genome Comparison, you have to fulfill three steps: 1) '''Select Reference Genome''' The reference genome is used as a basis for the comparison. All selected genomes (step 2) will be projected on this one. Click [[SEED_Viewer_Manual/OrganismSelect|here]] to see how to select an organism. 2) '''Select Comparison Organisms''' You can select maximal four organisms to project on the reference genome. 3) '''Compute''' Press '''compute''' to start the computation. This may take while, as the system computes a bidirectional BLAST comparison of each genome to the reference genome. === Result === At the top of the result page you will see a list of the genomes involved in the comparison again. After each comparison genome, there is a button '''BlastDotPlot''' that leads to a [[SEED_Viewer_Manual/BLASTDotPlot|dot plot of the BLAST comparison]] between the comparison organism and the reference genome. You can use the link '''change organism selection''' on top of the table if the selection does not fit. [[Image:MCGResulta.png]] The colored [[WebComponents/Table|table]] below shows the outcome of the bidirectional BLAST comparisons between each comparison genome and the reference genome, projected on the reference genome. The colors in the table depicts the '''Percent protein sequence identity''' of each gene to it's ortholog in the reference genome. The legend on top of the table describes the coloring. [[Image:MCGResultb.png]] The first three columns of the table refer to the chosen reference genome ('''Contig''', '''Gene''' and '''Length'''). The Gene ID links to the [[SEED_Viewer_Manual/Annotation|Annotation]] page for the feature. The best BLAST hit of the query feature in the comparison genome is shown in three columns in the table ('''Hit''', '''Contig''' and '''Gene'''). The color of the hit is determined by the percent identity of the query and the hit. No color means there is no hit. The '''Hit''' column contains a '-' (no hit), 'uni' or 'bi'. The '''bi''' stands for ''bidirectional best hit'', meaning that the reverse hit from the comparison genome to the reference genome is also the best hit (That's not always true if a genome contains many close paralogs for a feature). If it's not a bidirectional hit, it shows '''uni''' for uni-directional. Each feature ID is again linked to the feature's [[SEED_Viewer_Manual/Annotation|Annotation Page]]. Hovering over a cell in the table will show a tooltip with some information about the feature. The contents of the table can be exported in ''tab-separated format'' using the '''export''' button on top of the table. The filters below the buttons refer to the percent identity for the features of each genome. You can choose to filter the table for the percent identity above or below a certain value for each genome, and also in combination. Use the button '''clear all filters''' to reset the table. [[Image:MCGResultc.png]] The circular image right to the table is a whole genome view for the reference genome. Each circle represents a projection of a comparison genome to the reference genome, in the same order as in the table. Keep in mind that the table as well as the graphic only shows features of the comparison genomes, that are hit by the reference genome. The order of the features is determined by the reference genome. If you click on a line in the graphics, the table will update and show the area that was clicked in the graphic. The red circle in the graphic determines the area the table currently displays. [[Image:MCGResult2.png]] bca7e0581f15b2f8acf4e4403ced55d32abd1e42 0 1556 2242 2008-12-02T09:45:25Z DanielaBartels 10 wikitext text/x-wiki == BLAST Dot Plot == [[Image:BLASTDotPlot1.png]] [[Image:BLASTDotPlot2.png]] 718775fc53035d5e5dc029e05cedd0fda6f22f3a 2245 2242 2008-12-02T10:29:48Z DanielaBartels 10 /* BLAST Dot Plot */ wikitext text/x-wiki == BLAST Dot Plot == This page shows a bidirectional comparison of two genomes. The data computed for the comparison is a protein-based BLAST of the features of the two genomes. The dot plot displays all bidirectional protein hits between the two genomes. In the example, the two genomes are very close, which results in a diagonal line. If you are interested in a certain region of the plot, you can select a window in the plot using the left mouse button. The coordinates of the region are then put in the text fields above the graphics. You can view this region in the [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] for a genome using the button '''display region'''. [[Image:BLASTDotPlot1.png]] [[Image:BLASTDotPlot2.png]] c3de0951e0132771cabf2fe8ee6d59f43eace0e5 2246 2245 2008-12-02T10:40:47Z DanielaBartels 10 /* BLAST Dot Plot */ wikitext text/x-wiki == BLAST Dot Plot == This page shows a bidirectional comparison of two genomes. The data computed for the comparison is a protein-based BLAST of the features of the two genomes. The dot plot displays all bidirectional protein hits between the two genomes. In the example, the two genomes are very close, which results in a diagonal line. If you are interested in a certain region of the plot, you can select a window in the plot using the left mouse button. The coordinates of the region are then put in the text fields above the graphics. You can view this region in the [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] for a genome using the button '''display region'''. The region will be pre-selected in the Genome Browser. [[Image:BLASTDotPlot1.png]] [[Image:BLASTDotPlot2.png]] 94e93a56fe951fc9e12ce4fd8dca07fb6aa03f81 2247 2246 2008-12-02T10:41:10Z DanielaBartels 10 /* BLAST Dot Plot */ wikitext text/x-wiki == BLAST Dot Plot == This page shows a bidirectional comparison of two genomes. The data computed for the comparison is a protein-based BLAST of the features of the two genomes. The dot plot displays all bidirectional protein hits between the two genomes. In the example, the two genomes are very close, which results in a diagonal line. If you are interested in a certain region of the plot, you can select a window in the plot using the left mouse button. The coordinates of the region are then put in the text fields above the graphics. You can view this region in the [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] for a genome using the button '''display region'''. The region will be pre-selected in the [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]]. [[Image:BLASTDotPlot1.png]] [[Image:BLASTDotPlot2.png]] dfb986f857278fb4f484ece87714ddab6e0d2836 6 1557 2243 2008-12-02T09:45:50Z DanielaBartels 10 wikitext text/x-wiki da39a3ee5e6b4b0d3255bfef95601890afd80709 6 1558 2244 2008-12-02T09:46:10Z DanielaBartels 10 wikitext text/x-wiki da39a3ee5e6b4b0d3255bfef95601890afd80709 0 1559 2248 2008-12-02T11:26:14Z DanielaBartels 10 wikitext text/x-wiki == Compare Metabolic Reconstruction == This comparison is done on basis of the functions of all features of two genomes. The reference genome is called '''Organism A''', the comparison genome '''Organism B'''. The first column of the table ('''Presence''') tells you for each line if the function is present in ''A'', ''B'', or ''A and B''. The next three columns describe the subsystem the functional role belongs to. If a functional role is present in more than one subsystem, '''[...]'''. If a feature is assigned with more than one functional role (multi-functional), '''[...]'''. 3358a5837bfb31a366913812d420caf325d38339 2249 2248 2008-12-02T11:31:27Z DanielaBartels 10 /* Compare Metabolic Reconstruction */ wikitext text/x-wiki == Compare Metabolic Reconstruction == This comparison is done on basis of the functions of all features of two genomes. The reference genome is called '''Organism A''', the comparison genome '''Organism B'''. The first column of the table ('''Presence''') tells you for each function, if it is present in ''A'', ''B'', or ''A and B''. The next three columns ('''Category''', '''Subcategory''' and '''Subsystem''') describe the subsystem the functional role belongs to. If a functional role is present in more than one subsystem, '''[...]'''. The functional role itself is displayed in column 5 ('''Role'''). The feature(s) that implement(s) the functional role in '''Organism A''' will appear in the next column. The following column '''SS active A''' tells you if the subsystem listed in the line is active in the Organism A, meaning that it has a valid variant code. The same information is shown for '''Organism B''' in the next two columns. If a feature is assigned with more than one functional role (multi-functional), '''[...]'''. 7ddf2fcd9d9242b896008396f6b4004d0b6638e4 2250 2249 2008-12-02T11:32:00Z DanielaBartels 10 /* Compare Metabolic Reconstruction */ wikitext text/x-wiki == Compare Metabolic Reconstruction == This comparison is done on basis of the functions of all features of two genomes. The reference genome is called '''Organism A''', the comparison genome '''Organism B'''. The first column of the table ('''Presence''') tells you for each function, if it is present in ''A'', ''B'', or ''A and B''. The next three columns ('''Category''', '''Subcategory''' and '''Subsystem''') describe the subsystem the functional role belongs to. If a functional role is present in more than one subsystem, '''[...]'''. The functional role itself is displayed in column 5 ('''Role'''). The feature(s) that implement(s) the functional role in '''Organism A''' will appear in the next column. The following column '''SS active A''' tells you if the subsystem listed in the line is active in the Organism A, meaning that it has a valid variant code. The same information is shown for '''Organism B''' in the next two columns. If a feature is assigned with more than one functional role (multi-functional), '''[...]'''. [[Image:CompareMetaReconst]] a4df34ce2339c610674314a8ee2ed6011f27321a 2252 2250 2008-12-02T11:32:40Z DanielaBartels 10 /* Compare Metabolic Reconstruction */ wikitext text/x-wiki == Compare Metabolic Reconstruction == This comparison is done on basis of the functions of all features of two genomes. The reference genome is called '''Organism A''', the comparison genome '''Organism B'''. The first column of the table ('''Presence''') tells you for each function, if it is present in ''A'', ''B'', or ''A and B''. The next three columns ('''Category''', '''Subcategory''' and '''Subsystem''') describe the subsystem the functional role belongs to. If a functional role is present in more than one subsystem, '''[...]'''. The functional role itself is displayed in column 5 ('''Role'''). The feature(s) that implement(s) the functional role in '''Organism A''' will appear in the next column. The following column '''SS active A''' tells you if the subsystem listed in the line is active in the Organism A, meaning that it has a valid variant code. The same information is shown for '''Organism B''' in the next two columns. If a feature is assigned with more than one functional role (multi-functional), '''[...]'''. [[Image:CompareMetaReconst.png]] e9480074bab62a9b621fa070732ac8efffa5091d 2253 2252 2008-12-02T11:34:43Z DanielaBartels 10 /* Compare Metabolic Reconstruction */ wikitext text/x-wiki == Compare Metabolic Reconstruction == This comparison is done on basis of the functions of all features of two genomes. The reference genome is called '''Organism A''', the comparison genome '''Organism B'''. The first column of the table ('''Presence''') tells you for each function, if it is present in ''A'', ''B'', or ''A and B''. The next three columns ('''Category''', '''Subcategory''' and '''Subsystem''') describe the subsystem the functional role belongs to. If a functional role is present in more than one subsystem, '''[...]'''. The functional role itself is displayed in column 5 ('''Role'''). The feature(s) that implement(s) the functional role in '''Organism A''' will appear in the next column. They are linked to the [[SEED_Viewer_Manual/Annotation|Annotation Page]] for that feature. The following column '''SS active A''' tells you if the subsystem listed in the line is active in the Organism A, meaning that it has a valid variant code. The same information is shown for '''Organism B''' in the next two columns. If a role is not present for one of the organisms, a '''Find''' button will be displayed instead of the feature id. '''[...]'''. If a feature is assigned with more than one functional role (multi-functional), '''[...]'''. [[Image:CompareMetaReconst.png]] bd3f561ece8b30c94b967b01488ed95c48bec0c6 2254 2253 2008-12-02T14:25:48Z DanielaBartels 10 /* Compare Metabolic Reconstruction */ wikitext text/x-wiki == Compare Metabolic Reconstruction == This comparison is done on basis of the functions of all features of two genomes. The reference genome is called '''Organism A''', the comparison genome '''Organism B'''. The first column of the table ('''Presence''') tells you for each function, if it is present in ''A'', ''B'', or ''A and B''. The next three columns ('''Category''', '''Subcategory''' and '''Subsystem''') describe the subsystem the functional role belongs to. The functional role itself is displayed in column 5 ('''Role'''). The feature(s) that implement(s) the functional role in '''Organism A''' will appear in the next column. They are linked to the [[SEED_Viewer_Manual/Annotation|Annotation Page]] for that feature. The following column '''SS active A''' tells you if the subsystem listed in the line is active in the Organism A, meaning that it has a valid variant code. The same information is shown for '''Organism B''' in the next two columns. If a role is not present for one of the organisms, a '''Find''' button will be displayed instead of the feature id. It leads to the [[SEED_Viewer_Manual/SearchGene|Search Gene Page]]. Here, you can search for a candidate for the function. If a feature is assigned with more than one functional role (multi-functional), it will appear once for each function in the table. [[Image:CompareMetaReconst.png]] 3bf0e50d4df6dd0e1e546261366bfd2ef51eab7a 2255 2254 2008-12-02T14:32:30Z DanielaBartels 10 /* Compare Metabolic Reconstruction */ wikitext text/x-wiki == Compare Metabolic Reconstruction == This comparison is done on basis of the functions of all features of two genomes. The reference genome is called '''Organism A''', the comparison genome '''Organism B'''. Entering the page, you have already defined an '''Organism A''', as you followed a link e.g. from an [[SEED_Viewer_Manual/OrganismPage|Organism Page]] of the '''Organism A'''. Now you have to choose your '''Organism B''' using the [[SEED_Viewer_Manual/OrganismSelect|Organism Select]] on the page. Click '''select''' to start the computation. The resulting page will start with a header line showing the two genomes to compare. Behind the header, you find a button '''select other''' if you don't like the comparison genome. It will open an [[SEED_Viewer_Manual/OrganismSelect|Organism Select]] to choose another comparison organism. [[Image:CompareMetaResult.png]] The first column of the table ('''Presence''') tells you for each function, if it is present in ''A'', ''B'', or ''A and B''. The next three columns ('''Category''', '''Subcategory''' and '''Subsystem''') describe the subsystem the functional role belongs to. The functional role itself is displayed in column 5 ('''Role'''). The feature(s) that implement(s) the functional role in '''Organism A''' will appear in the next column. They are linked to the [[SEED_Viewer_Manual/Annotation|Annotation Page]] for that feature. The following column '''SS active A''' tells you if the subsystem listed in the line is active in the Organism A, meaning that it has a valid variant code. The same information is shown for '''Organism B''' in the next two columns. If a role is not present for one of the organisms, a '''Find''' button will be displayed instead of the feature id. It leads to the [[SEED_Viewer_Manual/SearchGene|Search Gene Page]]. Here, you can search for a candidate for the function. If a feature is assigned with more than one functional role (multi-functional), it will appear once for each function in the table. [[Image:CompareMetaReconst.png]] abd4860bbdcdf1f231ac9df4a257184147f274f4 2257 2255 2008-12-02T14:43:54Z DanielaBartels 10 /* Compare Metabolic Reconstruction */ wikitext text/x-wiki == Compare Metabolic Reconstruction == This comparison is done on basis of the functions of all features of two genomes. The reference genome is called '''Organism A''', the comparison genome '''Organism B'''. Entering the page, you have already defined an '''Organism A''', as you followed a link e.g. from an [[SEED_Viewer_Manual/OrganismPage|Organism Page]] of the '''Organism A'''. Now you have to choose your '''Organism B''' using the [[SEED_Viewer_Manual/OrganismSelect|Organism Select]] on the page. Click '''select''' to start the computation. The resulting page will start with a header line showing the two genomes to compare. Behind the header, you find a button '''select other''' if you don't like the comparison genome. It will open an [[SEED_Viewer_Manual/OrganismSelect|Organism Select]] to choose another comparison organism. [[Image:CompareMetaResult.png]] The first column of the [[WebComponents/Table|table]] ('''Presence''') tells you for each function, if it is present in ''A'', ''B'', or ''A and B''. The next three columns ('''Category''', '''Subcategory''' and '''Subsystem''') describe the subsystem the functional role belongs to. The functional role itself is displayed in column 5 ('''Role'''). The feature(s) that implement(s) the functional role in '''Organism A''' will appear in the next column. They are linked to the [[SEED_Viewer_Manual/Annotation|Annotation Page]] for that feature. The following column '''SS active A''' tells you if the subsystem listed in the line is active in the Organism A, meaning that it has a valid variant code. The same information is shown for '''Organism B''' in the next two columns. If a role is not present for one of the organisms, a '''Find''' button will be displayed instead of the feature id. It leads to the [[SEED_Viewer_Manual/SearchGene|Search Gene Page]]. Here, you can search for a candidate for the function. If a feature is assigned with more than one functional role (multi-functional), it will appear once for each function in the table. You can export the contents of the table in ''tab-separated format'' using the '''save to file''' button. [[Image:CompareMetaReconst.png]] df31eb62e1cb543f4e1f22455c997ca9dc6c5782 6 1560 2251 2008-12-02T11:32:27Z DanielaBartels 10 wikitext text/x-wiki da39a3ee5e6b4b0d3255bfef95601890afd80709 6 1561 2256 2008-12-02T14:32:45Z DanielaBartels 10 wikitext text/x-wiki da39a3ee5e6b4b0d3255bfef95601890afd80709 0 1466 2258 2226 2008-12-02T14:45:03Z DanielaBartels 10 /* Main pages of the SeedViewer */ wikitext text/x-wiki == Main pages of the SeedViewer == ''' [[SEED_Viewer_Manual|Home Page]] ''' ''' [[SEED_Viewer_Manual/Menu|Menu]] ''' ''' [[SEED_Viewer_Manual/SubsystemSelect|Subsystem Select]] ''' '''[[SEED_Viewer_Manual/Subsystems|Subsystems]]''' '''[[SEED_Viewer_Manual/FunctionalRoles|Functional Role]]''' '''[[SEED_Viewer_Manual/FIGfamViewer|FIGfam Viewer]]''' '''[[SEED_Viewer_Manual/Annotation|Annotation]]''' '''[[SEED_Viewer_Manual/Evidence|Evidence]]''' '''[[SEED_Viewer_Manual/BLASTOrganism|BLAST against an organism]]''' '''[[SEED_Viewer_Manual/ShowSeqs|Sequence]]''' '''[[SEED_Viewer_Manual/GenomeBrowser|Browse Genome]]''' '''[[SEED_Viewer_Manual/OrganismSelect|Organism Select]]''' '''[[SEED_Viewer_Manual/OrganismPage|Organism Page]]''' '''[[SEED_Viewer_Manual/KEGG|KEGG]]''' '''[[SEED_Viewer_Manual/HomologClusters|Homolog Clusters]]''' '''[[SEED_Viewer_Manual/CompareMetabolicReconstruction|Compare Metabolic Reconstruction]]''' '''[[SEED_Viewer_Manual/MultiGenomeCompare|Multi Genome Compare]]''' '''[[SEED_Viewer_Manual/BLASTDotPlot|BLAST Dot Plot]]''' '''[[SEED_Viewer_Manual/SearchGene|Search Gene]]''' 5d078a26c8c11501468b070ece93e2ad9036778a 2275 2258 2008-12-02T17:16:27Z DanielaBartels 10 /* Main pages of the SeedViewer */ wikitext text/x-wiki == Main pages of the SeedViewer == ''' [[SEED_Viewer_Manual|Home Page]] ''' ''' [[SEED_Viewer_Manual/Menu|Menu]] ''' ''' [[SEED_Viewer_Manual/SubsystemSelect|Subsystem Select]] ''' '''[[SEED_Viewer_Manual/Subsystems|Subsystems]]''' '''[[SEED_Viewer_Manual/FunctionalRoles|Functional Role]]''' '''[[SEED_Viewer_Manual/FIGfamViewer|FIGfam Viewer]]''' '''[[SEED_Viewer_Manual/Annotation|Annotation]]''' '''[[SEED_Viewer_Manual/Evidence|Evidence]]''' '''[[SEED_Viewer_Manual/BLASTOrganism|BLAST against an organism]]''' '''[[SEED_Viewer_Manual/ShowSeqs|Sequence]]''' '''[[SEED_Viewer_Manual/ContigView|Contig View]]''' '''[[SEED_Viewer_Manual/GenomeBrowser|Browse Genome]]''' '''[[SEED_Viewer_Manual/OrganismSelect|Organism Select]]''' '''[[SEED_Viewer_Manual/OrganismPage|Organism Page]]''' '''[[SEED_Viewer_Manual/KEGG|KEGG]]''' '''[[SEED_Viewer_Manual/HomologClusters|Homolog Clusters]]''' '''[[SEED_Viewer_Manual/CompareMetabolicReconstruction|Compare Metabolic Reconstruction]]''' '''[[SEED_Viewer_Manual/MultiGenomeCompare|Multi Genome Compare]]''' '''[[SEED_Viewer_Manual/BLASTDotPlot|BLAST Dot Plot]]''' '''[[SEED_Viewer_Manual/SearchGene|Search Gene]]''' deaac6e018cb9f312a2ec028e08c68f73eba3eb1 0 1562 2259 2008-12-02T14:56:05Z DanielaBartels 10 wikitext text/x-wiki == Search Gene == In this page you can search for a function in a genome in the context of a subsystem. Two ways of looking for a candidate feature for the function are provided: Looking for already existing features in the genome using a protein-based BLAST search, and trying to find candidates via a translated BLAST search against the DNA sequence of the whole genome. In both cases, a candidate feature is selected (or given to the page) from already existing features with assigned with the functional role that are part of the given subsystem. === Candidate genes found by Similarity (BLAST)? === [[Image:SearchGene1.png]] === Is the gene maybe not called? === [[Image:SearchGene2.png]] b643e2c69e4d891e869b1a6ab9d4b60af3260d99 2262 2259 2008-12-02T15:41:37Z DanielaBartels 10 /* Search Gene */ wikitext text/x-wiki == Search Gene == In this page you can search for a function in a genome in the context of a subsystem. Two ways of looking for a candidate feature for the function are provided: Looking for already existing features in the genome using a protein-based BLAST search, and trying to find candidates via a translated BLAST search against the DNA sequence of the whole genome. In both cases, '''reference feature(s)''' are selected (or given to the page) from already existing features with assigned with the functional role that are part of the given subsystem. === Candidate genes found by Similarity (BLAST)? === This part looks for [[Glossary#Similarities|Similarities]] of all '''reference feature''' (features in the subsystem that are assigned with the function) to the features of the selected genome. The output [[WebComponent/Table|table]] lists the E-Value ('''P-Sc'''), the reference feature that was hit ('''PEG'''), the length ('''Len''') of the hit feature, the current function of the hit feature ('''Current fn'''), as well as the query feature ('''Matched peg'''), its length ('''Len'''), and its '''Function'''. [[Image:SearchGene1.png]] === Is the gene maybe not called? === [[Image:SearchGene2.png]] c02a925c5b9f98c44470329d0763c29534bb49ec 2263 2262 2008-12-02T15:56:50Z DanielaBartels 10 /* Candidate genes found by Similarity (BLAST)? */ wikitext text/x-wiki == Search Gene == In this page you can search for a function in a genome in the context of a subsystem. Two ways of looking for a candidate feature for the function are provided: Looking for already existing features in the genome using a protein-based BLAST search, and trying to find candidates via a translated BLAST search against the DNA sequence of the whole genome. In both cases, '''reference feature(s)''' are selected (or given to the page) from already existing features with assigned with the functional role that are part of the given subsystem. === Candidate genes found by Similarity (BLAST)? === This part looks for [[Glossary#Similarities|Similarities]] of all '''reference feature''' (features in the subsystem that are assigned with the function) to the features of the selected genome. The output [[WebComponents/Table|table]] lists the E-Value ('''P-Sc'''), the reference feature that was hit ('''PEG'''), the length ('''Len''') of the hit feature, the current function of the hit feature ('''Current fn'''), as well as the query feature ('''Matched peg'''), its length ('''Len'''), and its '''Function'''. [[Image:SearchGene1.png]] === Is the gene maybe not called? === [[Image:SearchGene2.png]] a11614527fe86bdbff5212b3abea8b3d4af67ea5 2264 2263 2008-12-02T16:14:59Z DanielaBartels 10 /* Search Gene */ wikitext text/x-wiki == Search Gene == In this page you can search for a function in a genome in the context of a subsystem. Two ways of looking for a candidate feature for the function are provided: Looking for already existing features in the genome using a protein-based BLAST search, and trying to find candidates via a translated BLAST search against the DNA sequence of the whole genome. In both cases, '''reference feature(s)''' are selected (or given to the page) from already existing features with assigned with the functional role that are part of the given subsystem. === Candidate genes found by Similarity (BLAST)? === This part looks for [[Glossary#Similarities|Similarities]] of all '''reference feature''' (features in the subsystem that are assigned with the function) to the features of the selected genome. The output [[WebComponents/Table|table]] lists the E-Value ('''P-Sc'''), the reference feature that was hit ('''PEG'''), the length ('''Len''') of the hit feature, the current function of the hit feature ('''Current fn'''), as well as the query feature ('''Matched peg'''), its length ('''Len'''), and its '''Function'''. [[Image:SearchGene1.png]] === Is the gene maybe not called? === In this case, a '''reference feature''' is used for a translated BLAST search against the whole genome sequence of the genome. On the top of the section, you can find a link to the used query feature. It leads to the [[SEED_Viewer_Manual/Annotation|Annotation Page]]. You can select a different query feature using the drop down box and click the button '''Take this gene for tblastn search'''. The graphic shows the result of the tblastn search. It shows all found hit reagions. The hit is marked with a '''Q''' in the graphic. The region displays all features in the hit regions, colored by the frame each feature is in (See legend on top of the graphic). Dark colors mark that the features belong to the context subsystem. This way, you can see if the hit clusters wiht other features of the subsystem. [[Image:SearchGene2.png]] 84c6558f17010c2cf0f729a49fb4b4e2c93e47a1 2265 2264 2008-12-02T16:17:15Z DanielaBartels 10 /* Is the gene maybe not called? */ wikitext text/x-wiki == Search Gene == In this page you can search for a function in a genome in the context of a subsystem. Two ways of looking for a candidate feature for the function are provided: Looking for already existing features in the genome using a protein-based BLAST search, and trying to find candidates via a translated BLAST search against the DNA sequence of the whole genome. In both cases, '''reference feature(s)''' are selected (or given to the page) from already existing features with assigned with the functional role that are part of the given subsystem. === Candidate genes found by Similarity (BLAST)? === This part looks for [[Glossary#Similarities|Similarities]] of all '''reference feature''' (features in the subsystem that are assigned with the function) to the features of the selected genome. The output [[WebComponents/Table|table]] lists the E-Value ('''P-Sc'''), the reference feature that was hit ('''PEG'''), the length ('''Len''') of the hit feature, the current function of the hit feature ('''Current fn'''), as well as the query feature ('''Matched peg'''), its length ('''Len'''), and its '''Function'''. [[Image:SearchGene1.png]] === Is the gene maybe not called? === In this case, a '''reference feature''' is used for a translated BLAST search against the whole genome sequence of the genome. On the top of the section, you can find a link to the used query feature. It leads to the [[SEED_Viewer_Manual/Annotation|Annotation Page]]. You can select a different query feature using the drop down box and click the button '''Take this gene for tblastn search'''. The graphic shows the result of the tblastn search. It shows all found hit reagions. The hit is marked with a '''Q''' in the graphic. The region displays all features in the hit regions, colored by the frame each feature is in (See legend on top of the graphic). Dark colors mark that the features belong to the context subsystem. This way, you can see if the hit clusters with other features of the subsystem. If the hit ('''Q''') overlaps with an existing feature in the same frame, this feature might be the candidate you look for. [[Image:SearchGene2.png]] 43fcc4527560a14eace647a4ff09e992cc3d552e 2266 2265 2008-12-02T16:19:58Z DanielaBartels 10 /* Search Gene */ wikitext text/x-wiki == Search Gene == In this page you can search for a function in a genome in the context of a subsystem. Two ways of looking for a candidate feature for the function are provided: Looking for already existing features in the genome using a protein-based BLAST search, and trying to find candidates via a translated BLAST search against the DNA sequence of the whole genome. In both cases, '''reference feature(s)''' are selected (or given to the page) from already existing features with assigned with the functional role that are part of the given subsystem. If you are logged in and you have the right to annotate the genome, you will see additional annotation capabilities on this page (described [[here]]. === Candidate genes found by Similarity (BLAST)? === This part looks for [[Glossary#Similarities|Similarities]] of all '''reference feature''' (features in the subsystem that are assigned with the function) to the features of the selected genome. The output [[WebComponents/Table|table]] lists the E-Value ('''P-Sc'''), the reference feature that was hit ('''PEG'''), the length ('''Len''') of the hit feature, the current function of the hit feature ('''Current fn'''), as well as the query feature ('''Matched peg'''), its length ('''Len'''), and its '''Function'''. [[Image:SearchGene1.png]] === Is the gene maybe not called? === In this case, a '''reference feature''' is used for a translated BLAST search against the whole genome sequence of the genome. On the top of the section, you can find a link to the used query feature. It leads to the [[SEED_Viewer_Manual/Annotation|Annotation Page]]. You can select a different query feature using the drop down box and click the button '''Take this gene for tblastn search'''. The graphic shows the result of the tblastn search. It shows all found hit reagions. The hit is marked with a '''Q''' in the graphic. The region displays all features in the hit regions, colored by the frame each feature is in (See legend on top of the graphic). Dark colors mark that the features belong to the context subsystem. This way, you can see if the hit clusters with other features of the subsystem. If the hit ('''Q''') overlaps with an existing feature in the same frame, this feature might be the candidate you look for. [[Image:SearchGene2.png]] b3a60cf5246e7721ffaeecb82806c9fa75667c10 2267 2266 2008-12-02T16:21:05Z DanielaBartels 10 /* Search Gene */ wikitext text/x-wiki == Search Gene == In this page you can search for a function in a genome in the context of a subsystem. Two ways of looking for a candidate feature for the function are provided: Looking for already existing features in the genome using a protein-based BLAST search, and trying to find candidates via a translated BLAST search against the DNA sequence of the whole genome. In both cases, '''reference feature(s)''' are selected (or given to the page) from already existing features with assigned with the functional role that are part of the given subsystem. If you are logged in and you have the right to annotate the genome, you will see additional annotation capabilities on this page (described [[SEED_Viewer_Manual/Editing_Capabilities/SearchGene|here]]. === Candidate genes found by Similarity (BLAST)? === This part looks for [[Glossary#Similarities|Similarities]] of all '''reference feature''' (features in the subsystem that are assigned with the function) to the features of the selected genome. The output [[WebComponents/Table|table]] lists the E-Value ('''P-Sc'''), the reference feature that was hit ('''PEG'''), the length ('''Len''') of the hit feature, the current function of the hit feature ('''Current fn'''), as well as the query feature ('''Matched peg'''), its length ('''Len'''), and its '''Function'''. [[Image:SearchGene1.png]] === Is the gene maybe not called? === In this case, a '''reference feature''' is used for a translated BLAST search against the whole genome sequence of the genome. On the top of the section, you can find a link to the used query feature. It leads to the [[SEED_Viewer_Manual/Annotation|Annotation Page]]. You can select a different query feature using the drop down box and click the button '''Take this gene for tblastn search'''. The graphic shows the result of the tblastn search. It shows all found hit reagions. The hit is marked with a '''Q''' in the graphic. The region displays all features in the hit regions, colored by the frame each feature is in (See legend on top of the graphic). Dark colors mark that the features belong to the context subsystem. This way, you can see if the hit clusters with other features of the subsystem. If the hit ('''Q''') overlaps with an existing feature in the same frame, this feature might be the candidate you look for. [[Image:SearchGene2.png]] 6aec7eedd68e8147eb211f332db17ce4348af7be 2268 2267 2008-12-02T16:21:16Z DanielaBartels 10 /* Search Gene */ wikitext text/x-wiki == Search Gene == In this page you can search for a function in a genome in the context of a subsystem. Two ways of looking for a candidate feature for the function are provided: Looking for already existing features in the genome using a protein-based BLAST search, and trying to find candidates via a translated BLAST search against the DNA sequence of the whole genome. In both cases, '''reference feature(s)''' are selected (or given to the page) from already existing features with assigned with the functional role that are part of the given subsystem. If you are logged in and you have the right to annotate the genome, you will see additional annotation capabilities on this page (described [[SEED_Viewer_Manual/Editing_Capabilities/SearchGene|here]]). === Candidate genes found by Similarity (BLAST)? === This part looks for [[Glossary#Similarities|Similarities]] of all '''reference feature''' (features in the subsystem that are assigned with the function) to the features of the selected genome. The output [[WebComponents/Table|table]] lists the E-Value ('''P-Sc'''), the reference feature that was hit ('''PEG'''), the length ('''Len''') of the hit feature, the current function of the hit feature ('''Current fn'''), as well as the query feature ('''Matched peg'''), its length ('''Len'''), and its '''Function'''. [[Image:SearchGene1.png]] === Is the gene maybe not called? === In this case, a '''reference feature''' is used for a translated BLAST search against the whole genome sequence of the genome. On the top of the section, you can find a link to the used query feature. It leads to the [[SEED_Viewer_Manual/Annotation|Annotation Page]]. You can select a different query feature using the drop down box and click the button '''Take this gene for tblastn search'''. The graphic shows the result of the tblastn search. It shows all found hit reagions. The hit is marked with a '''Q''' in the graphic. The region displays all features in the hit regions, colored by the frame each feature is in (See legend on top of the graphic). Dark colors mark that the features belong to the context subsystem. This way, you can see if the hit clusters with other features of the subsystem. If the hit ('''Q''') overlaps with an existing feature in the same frame, this feature might be the candidate you look for. [[Image:SearchGene2.png]] 6b375c6e7609eae7fb662b8d842c296ac989d711 6 1563 2260 2008-12-02T14:56:24Z DanielaBartels 10 wikitext text/x-wiki da39a3ee5e6b4b0d3255bfef95601890afd80709 6 1564 2261 2008-12-02T14:56:46Z DanielaBartels 10 wikitext text/x-wiki da39a3ee5e6b4b0d3255bfef95601890afd80709 0 1565 2269 2008-12-02T16:23:23Z DanielaBartels 10 wikitext text/x-wiki == Editing capabilities in the SeedViewer == [[SEED_Viewer_Manual/Editing_Capabilities/Annotation|Annotation Page]] [[SEED_Viewer_Manual/Editing_Capabilities/Annotate Cluster|Annotate Cluster Page]] [[SEED_Viewer_Manual/Editing_Capabilities/Evidence|Evidence Page]] [[SEED_Viewer_Manual/Editing_Capabilities/SearchGene|Search Gene Page]] 9378e6f900bde6aa4819e4aa5fe397db1fa73358 2270 2269 2008-12-02T16:26:33Z DanielaBartels 10 /* Editing capabilities in the SeedViewer */ wikitext text/x-wiki == Editing capabilities in the SeedViewer == [[SEED_Viewer_Manual/Editing_Capabilities/Annotation|Annotation Page]] [[SEED_Viewer_Manual/Editing_Capabilities/ChromosomalClusters|Chromosomal Clusters Page]] [[SEED_Viewer_Manual/Editing_Capabilities/Evidence|Evidence Page]] [[SEED_Viewer_Manual/Editing_Capabilities/SearchGene|Search Gene Page]] 328f9d0c2b8ef978a7330a9ef37df1e0f4b367d9 0 1566 2271 2008-12-02T16:46:42Z DanielaBartels 10 wikitext text/x-wiki == Contig View == [[Image:ContigView1.png]] [[Image:ContigView2.png]] 6f4e11e88e7de037f26d89fae87b36f4bf944845 2274 2271 2008-12-02T17:15:21Z DanielaBartels 10 /* Contig View */ wikitext text/x-wiki == Contig View == This page shows a window of the Contig centered on a selected feature. The window is described in the top table. It names the '''Organism''' and '''Contig Length''' for the feature. The '''Start Base''' and '''End Base''' of the window and the resulting '''Region Length''' is shown. The '''Region GC Content''' is computed for that window. For the selected feature, the second table gives you the Protein ID ('''Protein of Interest Region'''), the '''Contig''' name, as well as the '''Start Codon Location''' and the '''Stop Codon Location'''. [[Image:ContigView1.png]] The graphic displays the window in a six-frame view. You can use the horizontal scroll bar to navigate the window. The DNA sequence for both strands is displayed in small colored letters. The four bases are colored as follows: ''t'' - blue, ''c'' - red, ''a'' - purple and ''g'' - green. Background colors are used to mark possible '''Start Codons''' (yellow) and '''Shine-Dalgarno sites''' (green). Above the forward strand DNA sequence, you can see the translated protein sequences for the three forward strands. A ''*'' marks a stop codon. Below the reverse-strand DNA sequence, the three reverse protein strands are shown. Protein features are displayed in form of boxes on the respective strand. The selected feature ('''Protein of interest''') gets a box with a red background, other features have a box with blue background. Below the six-frame view, you can find a '''Third GC Codon plot'''. The dotted line is the average GC content for the region. The colored lines are the GC content for the third Codon of the triplets for each strand. [[Image:ContigView2.png]] bd047ddccda8f0e09e3fac2baba7ddfaa3e09128 6 1567 2272 2008-12-02T16:46:56Z DanielaBartels 10 wikitext text/x-wiki da39a3ee5e6b4b0d3255bfef95601890afd80709 6 1568 2273 2008-12-02T16:47:13Z DanielaBartels 10 wikitext text/x-wiki da39a3ee5e6b4b0d3255bfef95601890afd80709 0 1569 2276 2008-12-03T14:28:42Z DanielaBartels 10 wikitext text/x-wiki == Kegg Maps == [[Image:KeggMapSelect.png]] [[Image:KeggMap.png]] [[Image:KeggOrgSelect.png]] [[Image:KeggOrgTable.png]] a1933642f3a0587e22cda5c8a3f79039d0cf5cdb 6 1570 2277 2008-12-03T14:37:23Z DanielaBartels 10 wikitext text/x-wiki da39a3ee5e6b4b0d3255bfef95601890afd80709 6 1571 2278 2008-12-03T14:37:39Z DanielaBartels 10 wikitext text/x-wiki da39a3ee5e6b4b0d3255bfef95601890afd80709 6 1572 2279 2008-12-03T14:37:56Z DanielaBartels 10 wikitext text/x-wiki da39a3ee5e6b4b0d3255bfef95601890afd80709 6 1573 2280 2008-12-03T14:38:13Z DanielaBartels 10 wikitext text/x-wiki da39a3ee5e6b4b0d3255bfef95601890afd80709 0 1466 2281 2275 2008-12-03T14:48:43Z DanielaBartels 10 /* Main pages of the SeedViewer */ wikitext text/x-wiki == Main pages of the SeedViewer == ''' [[SEED_Viewer_Manual|Home Page]] ''' ''' [[SEED_Viewer_Manual/Menu|Menu]] ''' ''' [[SEED_Viewer_Manual/SubsystemSelect|Subsystem Select]] ''' '''[[SEED_Viewer_Manual/Subsystems|Subsystems]]''' '''[[SEED_Viewer_Manual/FunctionalRoles|Functional Role]]''' '''[[SEED_Viewer_Manual/FIGfamViewer|FIGfam Viewer]]''' '''[[SEED_Viewer_Manual/Annotation|Annotation]]''' '''[[SEED_Viewer_Manual/Evidence|Evidence]]''' '''[[SEED_Viewer_Manual/BLASTOrganism|BLAST against an organism]]''' '''[[SEED_Viewer_Manual/ShowSeqs|Sequence]]''' '''[[SEED_Viewer_Manual/ContigView|Contig View]]''' '''[[SEED_Viewer_Manual/GenomeBrowser|Browse Genome]]''' '''[[SEED_Viewer_Manual/OrganismSelect|Organism Select]]''' '''[[SEED_Viewer_Manual/OrganismPage|Organism Page]]''' '''[[SEED_Viewer_Manual/KEGG|KEGG]]''' '''[[SEED_Viewer_Manual/HomologClusters|Homolog Clusters]]''' '''[[SEED_Viewer_Manual/CompareMetabolicReconstruction|Compare Metabolic Reconstruction]]''' '''[[SEED_Viewer_Manual/MultiGenomeCompare|Multi Genome Compare]]''' '''[[SEED_Viewer_Manual/BLASTDotPlot|BLAST Dot Plot]]''' '''[[SEED_Viewer_Manual/SearchGene|Search Gene]]''' '''[[SEED_Viewer_Manual/Scenarios|Scenarios]]''' a961b4ee322ebdb22017b89ab8d0373a02833d84 2312 2281 2008-12-03T18:22:15Z DanielaBartels 10 /* Main pages of the SeedViewer */ wikitext text/x-wiki == Main pages of the SeedViewer == '''[[SEED_Viewer_Manual|Home Page]]''' '''[[SEED_Viewer_Manual/Menu|Menu]]''' '''[[SEED_Viewer_Manual/Subsystems|Subsystems]]''' '''[[SEED_Viewer_Manual/FunctionalRoles|Functional Role]]''' '''[[SEED_Viewer_Manual/FIGfamViewer|FIGfam Viewer]]''' '''[[SEED_Viewer_Manual/Annotation|Annotation]]''' '''[[SEED_Viewer_Manual/Evidence|Evidence]]''' '''[[SEED_Viewer_Manual/BLASTOrganism|BLAST against an organism]]''' '''[[SEED_Viewer_Manual/ShowSeqs|Sequence]]''' '''[[SEED_Viewer_Manual/ContigView|Contig View]]''' '''[[SEED_Viewer_Manual/GenomeBrowser|Browse Genome]]''' '''[[SEED_Viewer_Manual/OrganismSelect|Organism Select]]''' '''[[SEED_Viewer_Manual/OrganismPage|Organism Page]]''' '''[[SEED_Viewer_Manual/KEGG|KEGG]]''' '''[[SEED_Viewer_Manual/HomologClusters|Homolog Clusters]]''' '''[[SEED_Viewer_Manual/CompareMetabolicReconstruction|Compare Metabolic Reconstruction]]''' '''[[SEED_Viewer_Manual/MultiGenomeCompare|Multi Genome Compare]]''' '''[[SEED_Viewer_Manual/BLASTDotPlot|BLAST Dot Plot]]''' '''[[SEED_Viewer_Manual/SearchGene|Search Gene]]''' '''[[SEED_Viewer_Manual/Scenarios|Scenarios]]''' 30782e0b17a2b25cd3b53f1713ef0ac9a1528533 0 1569 2282 2276 2008-12-03T14:53:57Z DanielaBartels 10 /* Kegg Maps */ wikitext text/x-wiki == Kegg Maps == This page allows you to view [http://www.genome.jp/kegg/ KEGG] maps and statistics for chosen organisms in the SEED. Usually, you enter this page from a page that had an organism defined. The chosen organism is stated in the header: [[Image:KeggMapHeader.png]] Entering the page, you will see the overview [http://www.genome.jp/kegg/ KEGG] map pre-selected, which is '''Metabolism'''. [[Image:KeggMapSelect.png]] [[Image:KeggMap.png]] [[Image:KeggOrgSelect.png]] [[Image:KeggOrgTable.png]] 09dd74450741130f36a758bcbe1806584680c6eb 2284 2282 2008-12-03T14:57:31Z DanielaBartels 10 /* Kegg Maps */ wikitext text/x-wiki == Kegg Maps == This page allows you to view [http://www.genome.jp/kegg/ KEGG] maps and statistics for chosen organisms in the SEED. Usually, you enter this page from a page that had an organism defined. The chosen organism is stated in the header: [[Image:KeggMapHeader.png]] Entering the page, you will see the overview [http://www.genome.jp/kegg/ KEGG] map pre-selected, which is '''Metabolism'''. In the following [[WebComponents/FilterSelect|Filter Select]] you can select another map. Press '''select''' to display the map in the graphic on the bottom of the page. [[Image:KeggMapSelect.png]] In the example, the [http://www.genome.jp/kegg/ KEGG] map '''Lysine [[Image:KeggMap.png]] [[Image:KeggOrgSelect.png]] [[Image:KeggOrgTable.png]] 923e075d473d5b1bad537d62452312cbc916c611 2285 2284 2008-12-03T15:16:14Z DanielaBartels 10 /* Kegg Maps */ wikitext text/x-wiki == Kegg Maps == This page allows you to view [http://www.genome.jp/kegg/ KEGG] maps and statistics for chosen organisms in the SEED. Usually, you enter this page from a page that had an organism defined. The chosen organism is stated in the header: [[Image:KeggMapHeader.png]] Entering the page, you will see the overview [http://www.genome.jp/kegg/ KEGG] map pre-selected, which is '''Metabolism'''. In the following [[WebComponents/FilterSelect|Filter Select]] you can select another map. Press '''select''' to display the map in the graphic on the bottom of the page. [[Image:KeggMapSelect.png]] In the example, the [http://www.genome.jp/kegg/ KEGG] map '''Lysine Biosynthesis''' was selected. The map shows the connections between the enzymes and the educts / products of the reactions the enzymes perform. The enzyme numbers (EC-Numbers) are connected to features in SEED organisms through the [[Glossary#Functional Role|functional role]] assignments to the features. The map is colored for the chosen organism (in this case ''Escherichia coli K12''). If the organism implements a functional role with the EC-number in the map, its box is colored in green, else white. The blue boxes in the map link to neighboring (connected) maps in the metabolism. [[Image:KeggMap.png]] You can view statistics for up to four additional organisms compared to the chosen organism. Select these organisms in the [[WebComponents/ListSelect|List Select]] top right on the page. Choose an organism and press the ''right arrow'' to select it. For unselecting it, choose it in the right box and press the ''left arrow''. After making your selection, press the '''select''' button on the left (same button as above). [[Image:KeggOrgSelect.png]] The statistics table will show all subcategories of the selected category for your organisms. For each subcategory, you can see the number of implemented EC-numbers in each organism, as well as the percent of total EC-numbers that are implemented as a green bar. The number links to the map of the subcategory and the organism. [[Image:KeggOrgTable.png]] dec0f609762cd4d8e60efc1d5dec3a27a15c33a8 2291 2285 2008-12-03T15:36:33Z DanielaBartels 10 /* Kegg Maps */ wikitext text/x-wiki == Kegg Maps == This page allows you to view [http://www.genome.jp/kegg/ KEGG] maps and statistics for chosen organisms in the SEED. Usually, you enter this page from a page that had an organism defined. The chosen organism is stated in the header: [[Image:KeggMapHeader.png]] Entering the page, you will see the overview [http://www.genome.jp/kegg/ KEGG] map pre-selected, which is '''Metabolism'''. In the following [[WebComponents/FilterSelect|Filter Select]] you can select another map. Press '''select''' to display the map in the graphic on the bottom of the page. [[Image:KeggMapSelect.png]] In the example, the [http://www.genome.jp/kegg/ KEGG] map '''Lysine Biosynthesis''' was selected. The map shows the connections between the enzymes and the educts / products of the reactions the enzymes perform. The enzyme numbers (EC-Numbers) are connected to features in SEED organisms through the [[Glossary#Functional Role|functional role]] assignments to the features. The map is colored for the chosen organism (in this case ''Escherichia coli K12''). If the organism implements a functional role with the EC-number in the map, its box is colored in green, else white. The blue boxes in the map link to neighboring (connected) maps in the metabolism. [[Image:KeggMap.png]] You can view statistics for up to four additional organisms compared to the chosen organism. Select these organisms in the [[WebComponents/ListSelect|List Select]] top right on the page. Choose an organism and press the ''right arrow'' to select it. For unselecting it, choose it in the right box and press the ''left arrow''. After making your selection, press the '''select''' button on the left (same button as above). [[Image:KeggOrgSelect.png]] The statistics table will show all connecting maps of the selected category for your organisms. For each map, you can see the number of implemented EC-numbers in each organism, as well as the percent of total EC-numbers that are implemented as a green bar. The number links to the connecting map for the organism. [[Image:KeggOrgTable.png]] e366149caae6770cdf69115a1e06bfbe33c8ef6e 6 1574 2283 2008-12-03T14:54:12Z DanielaBartels 10 wikitext text/x-wiki da39a3ee5e6b4b0d3255bfef95601890afd80709 0 1532 2286 2168 2008-12-03T15:17:24Z DanielaBartels 10 wikitext text/x-wiki [[WebComponents/ListSelect|List Select]] [[WebComponents/Login|LoginBox]] [[WebComponents/FilterSelect|Filter Select]] [[WebComponents/Table|Table]] [[WebComponents/Tabview|TabView]] 11dd72befbfbfd94a7d963c296f54cd0b6fb94d8 2292 2286 2008-12-03T15:41:25Z DanielaBartels 10 wikitext text/x-wiki == Web Components == '''Web Components''' are widgets that were developed in context of the SEED applications, e.g. the [[SEED_Viewer_Manual|SeedViewer]], the [[RAST_Tutorial|RAST]] and others. The components provide functionality that is needed on many pages. Most prominent components are the '''[[WebComponents/Table|Table]]''' and the '''[[WebComponents/Tabview|TabView]]'''. See a list of common components on how to use them: [[WebComponents/ListSelect|List Select]] [[WebComponents/Login|LoginBox]] [[WebComponents/FilterSelect|Filter Select]] [[WebComponents/Table|Table]] [[WebComponents/Tabview|TabView]] 629d771e47b62faadee983a5ba69648e30a1eaba 0 1575 2287 2008-12-03T15:19:07Z DanielaBartels 10 wikitext text/x-wiki == Filter Select == A '''Filter Select''' contains two components: a Text Box and a Select Box. [[Image:KeggMapSelect.png]] b941f721cb4b28e2595ad5ee408988c57e1f2427 2288 2287 2008-12-03T15:33:20Z DanielaBartels 10 /* Filter Select */ wikitext text/x-wiki == Filter Select == A '''Filter Select''' contains two components: a Text Box and a Select Box. The Select Box contains all options the user can select. If a Select Box is a ''multiple'' Select Box, you can select more than one option. Searching for an option can be done using the Text Box on top of the Select Box. If you start typing, the Filter Select will automatically remove all options that do not fit to the keyword, meaning that an infix search is done on the options and not-matching options are removed. In the example, you see a [http://www.genome.jp/kegg/ KEGG] map select you can find on the [[SEED_Viewer_Manual/KEGG|KEGG Page]] of the [[SEED_Viewer_Manual|SeedViewer]]. This Filter Select is not multiple, so that you can only choose one KEGG map from the list. [[Image:KeggMapSelect.png]] 4b3cac37253a2752b2f9796494fee3c705633e0c 2289 2288 2008-12-03T15:33:59Z DanielaBartels 10 /* Filter Select */ wikitext text/x-wiki == Filter Select == A '''Filter Select''' contains two components: a Text Box and a Select Box. The Select Box contains all options the user can select. Use the scroll bars to browse through the options. If a Select Box is a ''multiple'' Select Box, you can select more than one option. Searching for an option can be done using the Text Box on top of the Select Box. If you start typing, the Filter Select will automatically remove all options that do not fit to the keyword, meaning that an infix search is done on the options and not-matching options are removed. In the example, you see a [http://www.genome.jp/kegg/ KEGG] map select you can find on the [[SEED_Viewer_Manual/KEGG|KEGG Page]] of the [[SEED_Viewer_Manual|SeedViewer]]. This Filter Select is not multiple, so that you can only choose one KEGG map from the list. [[Image:KeggMapSelect.png]] f310bc2c3669467a15527e720061a852e94f8863 2290 2289 2008-12-03T15:34:11Z DanielaBartels 10 /* Filter Select */ wikitext text/x-wiki == Filter Select == A '''Filter Select''' contains two components: a Text Box and a Select Box. The Select Box contains all options the user can select. Use the scroll bar on the right to browse through the options. If a Select Box is a ''multiple'' Select Box, you can select more than one option. Searching for an option can be done using the Text Box on top of the Select Box. If you start typing, the Filter Select will automatically remove all options that do not fit to the keyword, meaning that an infix search is done on the options and not-matching options are removed. In the example, you see a [http://www.genome.jp/kegg/ KEGG] map select you can find on the [[SEED_Viewer_Manual/KEGG|KEGG Page]] of the [[SEED_Viewer_Manual|SeedViewer]]. This Filter Select is not multiple, so that you can only choose one KEGG map from the list. [[Image:KeggMapSelect.png]] 7a551c6d5cf60c86ee71101f9f89dd38971f758a 0 1478 2293 2099 2008-12-03T15:45:27Z DanielaBartels 10 /* Feature Tools */ wikitext text/x-wiki == Menu Overview == The menu is a small bar below the logo of each page. Most menus have submenus that can be accessed via hovering over the menu. Right-click the submenu you want to go to. If no submenu is present, you can directly click the menu itself. === Navigate Menu === This menu is present on every SeedViewer page. The first entry '''Startpage''' will lead to the SeedViewer [[SEED_Viewer_Manual|HomePage]]. '''Organisms''' will open the [[SEED_Viewer_Manual/OrganismSelect|Organism Select]] page. You will see an overview of all organisms in the SEED and are able to select one to view in detail. '''Subsystems''' will do the same for subsystems. '''FIGFams''' leads to an entry point for browsing [[SEED_Viewer_Manual/FIGfams|FIGfams]]. You can find more information about FIGfams [[Glossary#FIGfam|here]]. The '''BLAST Search''' links to the [[SEED_Viewer_Manual/BLASTOrganism|BLAST Page]]. You will be able to BLAST a sequence against an organism in the SEED. [[Image:MenuNav.png]] === Help Menu === This menu is also present on all SeedViewer pages. The first link '''What is the SEED''' will lead you to the [[Home_of_the_SEED|SEED Homepage]]. Clicking the second link '''How to use the SEED Viewer''' will get you to this wiki. '''Submitting data to SEED''' lets you browse the [[RAST_Tutorial|RAST Tutorial]]. '''Contact''' enables you to write an email to the SEED team. Clicking '''Register''' is the first step to get a user account. It will lead to the [[SEED_Viewer_Manual/Register|Register]] page. '''I forgot my password''' enables you to [[SEED_Viewer_Manual/RequestNewPassword|Request a new password]]. [[Image:MenuHelp.png]] === Organism Menu === In the context of a selected organism, an organism menu will appear. '''General Information''' will lead to the [[SEED_Viewer_Manual/OrganismPage|Organism Page]] of the selected organism. The '''Feature Table''' will open the [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] and show you the features present in that organism. '''Genome Browser''' leads to the [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] for the selected organism. Clicking '''Scenarios''' shows the [[SEED_Viewer_Manual/Scenarios|Scenarios]] page for your organism. '''Subsystems''' opens a page that lets you select subsystems. '''Export''' enables you to [[SEED_Viewer_Manual/Export|download]] the features of your organism. [[Image:MenuOrganism.png]] === Comparative Tools === This menu is also present whenever an organism is viewed. Different kinds of comparisons of your selected organism to other organisms are available here. '''Function based Comparison''' - The [[SEED_Viewer_Manual/CompareMetabolicReconstruction|Compare Metabolic Reconstruction]] will enable you to see the metabolic reconstruction of your selected organism against that of another one. The '''Sequence based Comparison''' [[SEED_Viewer_Manual/MultiGenomeCompare|Multi Genome Compare]] shows a table and a graphics comparing a selected set of organisms projected against your chosen one (BLAST-based). Use the '''KEGG Metabolic Analysis''' [[SEED_Viewer_Manual/KEGG|to project the metabolic capabilities]] of your organism on KEGG maps. Blasting against your organism is enabled using the '''[[SEED_Viewer_Manual/BLASTOrganism|BLAST Search]]'''. [[Image:CompTools.png]] === Feature Menu === Whenever a feature is defined on a SeedViewer page, you will find the '''Feature''' menu for that feature. The '''Feature Overview''' points to the [[SEED_Viewer_Manual/Annotation|Annotation]] page. It shows general information about the feature, als well as a Compare Regions View that displays the feature in its genomic context and in comparison to homologs in other genomes. '''DNA Sequence''' will open a page with the DNA Sequence of the feature (in FASTA format). '''DNA w/ flanking''' not only prints the DNA sequence of the feature, but also includes a user-defined number of bases upstream and downstream of the feature. '''Protein Sequence''' will show you the protein FASTA sequence (translated from the DNA sequence) of the feature. '''Feature Evidence vs. FIG''' and '''Feature Evidence vs. all DB''' link to the [[SEED_Viewer_Manual/Evidence|Evidence]] page. The difference between the two is that the evidence shown for the feature includes only evidence against features in the SEED or also against other databases (e.g. GenBank, SwissProt, UniProt and many others). The evidence page will also allow you to make this selection or change it there. [[Image:MenuFeature.png]] === Feature Tools === This menu is also present if a feature is defined. It lets the user run a variaty of tools using the feature sequence. These include tools that look for transmembrane helices (e.g. [http://www.cbs.dtu.dk/services/TMHMM/ TMHMM]), signal peptides (PSORT, SignalP), protein domains (e.g. InterPro, ProDom) and others. [[Image:MenuFeatTools.png]] === FIGfams Menu === On SeedViewer pages that deal with [[Glossary#FIGfam|FIGfams]], you will find an additional FIGfams menu. The '''Home''' link leads to the entry page to [[SEED_Viewer_Manual/FIGfams|FIGfams]]. The '''Release History''' will lead you to a [[SEED_Viewer_Manual/FIGfamsRelease|page]] containing a number of statistics about the current release of the FIGfams. '''Download''' will connect you to the FTP server to enable you to download the FIGfams. [[Image:MenuFIGfam.png]] cedf99c6a4bbd9a950c3c967a4fa5cfa78347277 2294 2293 2008-12-03T15:49:08Z DanielaBartels 10 /* Feature Tools */ wikitext text/x-wiki == Menu Overview == The menu is a small bar below the logo of each page. Most menus have submenus that can be accessed via hovering over the menu. Right-click the submenu you want to go to. If no submenu is present, you can directly click the menu itself. === Navigate Menu === This menu is present on every SeedViewer page. The first entry '''Startpage''' will lead to the SeedViewer [[SEED_Viewer_Manual|HomePage]]. '''Organisms''' will open the [[SEED_Viewer_Manual/OrganismSelect|Organism Select]] page. You will see an overview of all organisms in the SEED and are able to select one to view in detail. '''Subsystems''' will do the same for subsystems. '''FIGFams''' leads to an entry point for browsing [[SEED_Viewer_Manual/FIGfams|FIGfams]]. You can find more information about FIGfams [[Glossary#FIGfam|here]]. The '''BLAST Search''' links to the [[SEED_Viewer_Manual/BLASTOrganism|BLAST Page]]. You will be able to BLAST a sequence against an organism in the SEED. [[Image:MenuNav.png]] === Help Menu === This menu is also present on all SeedViewer pages. The first link '''What is the SEED''' will lead you to the [[Home_of_the_SEED|SEED Homepage]]. Clicking the second link '''How to use the SEED Viewer''' will get you to this wiki. '''Submitting data to SEED''' lets you browse the [[RAST_Tutorial|RAST Tutorial]]. '''Contact''' enables you to write an email to the SEED team. Clicking '''Register''' is the first step to get a user account. It will lead to the [[SEED_Viewer_Manual/Register|Register]] page. '''I forgot my password''' enables you to [[SEED_Viewer_Manual/RequestNewPassword|Request a new password]]. [[Image:MenuHelp.png]] === Organism Menu === In the context of a selected organism, an organism menu will appear. '''General Information''' will lead to the [[SEED_Viewer_Manual/OrganismPage|Organism Page]] of the selected organism. The '''Feature Table''' will open the [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] and show you the features present in that organism. '''Genome Browser''' leads to the [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] for the selected organism. Clicking '''Scenarios''' shows the [[SEED_Viewer_Manual/Scenarios|Scenarios]] page for your organism. '''Subsystems''' opens a page that lets you select subsystems. '''Export''' enables you to [[SEED_Viewer_Manual/Export|download]] the features of your organism. [[Image:MenuOrganism.png]] === Comparative Tools === This menu is also present whenever an organism is viewed. Different kinds of comparisons of your selected organism to other organisms are available here. '''Function based Comparison''' - The [[SEED_Viewer_Manual/CompareMetabolicReconstruction|Compare Metabolic Reconstruction]] will enable you to see the metabolic reconstruction of your selected organism against that of another one. The '''Sequence based Comparison''' [[SEED_Viewer_Manual/MultiGenomeCompare|Multi Genome Compare]] shows a table and a graphics comparing a selected set of organisms projected against your chosen one (BLAST-based). Use the '''KEGG Metabolic Analysis''' [[SEED_Viewer_Manual/KEGG|to project the metabolic capabilities]] of your organism on KEGG maps. Blasting against your organism is enabled using the '''[[SEED_Viewer_Manual/BLASTOrganism|BLAST Search]]'''. [[Image:CompTools.png]] === Feature Menu === Whenever a feature is defined on a SeedViewer page, you will find the '''Feature''' menu for that feature. The '''Feature Overview''' points to the [[SEED_Viewer_Manual/Annotation|Annotation]] page. It shows general information about the feature, als well as a Compare Regions View that displays the feature in its genomic context and in comparison to homologs in other genomes. '''DNA Sequence''' will open a page with the DNA Sequence of the feature (in FASTA format). '''DNA w/ flanking''' not only prints the DNA sequence of the feature, but also includes a user-defined number of bases upstream and downstream of the feature. '''Protein Sequence''' will show you the protein FASTA sequence (translated from the DNA sequence) of the feature. '''Feature Evidence vs. FIG''' and '''Feature Evidence vs. all DB''' link to the [[SEED_Viewer_Manual/Evidence|Evidence]] page. The difference between the two is that the evidence shown for the feature includes only evidence against features in the SEED or also against other databases (e.g. GenBank, SwissProt, UniProt and many others). The evidence page will also allow you to make this selection or change it there. [[Image:MenuFeature.png]] === Feature Tools === This menu is also present if a feature is defined. It lets the user run a variaty of tools using the feature sequence. These include tools that look for transmembrane helices (e.g. [http://www.cbs.dtu.dk/services/TMHMM/ TMHMM]), signal peptides ([http://www.psort.org/ PSORT], [http://www.cbs.dtu.dk/services/SignalP/ SignalP]), protein domains (e.g. [http://www.ebi.ac.uk/interpro/ InterPro], ProDom) and others. [[Image:MenuFeatTools.png]] === FIGfams Menu === On SeedViewer pages that deal with [[Glossary#FIGfam|FIGfams]], you will find an additional FIGfams menu. The '''Home''' link leads to the entry page to [[SEED_Viewer_Manual/FIGfams|FIGfams]]. The '''Release History''' will lead you to a [[SEED_Viewer_Manual/FIGfamsRelease|page]] containing a number of statistics about the current release of the FIGfams. '''Download''' will connect you to the FTP server to enable you to download the FIGfams. [[Image:MenuFIGfam.png]] 5a18b68c120df1f8c69304ab2319e820ca89e3de 2295 2294 2008-12-03T15:50:02Z DanielaBartels 10 /* Feature Tools */ wikitext text/x-wiki == Menu Overview == The menu is a small bar below the logo of each page. Most menus have submenus that can be accessed via hovering over the menu. Right-click the submenu you want to go to. If no submenu is present, you can directly click the menu itself. === Navigate Menu === This menu is present on every SeedViewer page. The first entry '''Startpage''' will lead to the SeedViewer [[SEED_Viewer_Manual|HomePage]]. '''Organisms''' will open the [[SEED_Viewer_Manual/OrganismSelect|Organism Select]] page. You will see an overview of all organisms in the SEED and are able to select one to view in detail. '''Subsystems''' will do the same for subsystems. '''FIGFams''' leads to an entry point for browsing [[SEED_Viewer_Manual/FIGfams|FIGfams]]. You can find more information about FIGfams [[Glossary#FIGfam|here]]. The '''BLAST Search''' links to the [[SEED_Viewer_Manual/BLASTOrganism|BLAST Page]]. You will be able to BLAST a sequence against an organism in the SEED. [[Image:MenuNav.png]] === Help Menu === This menu is also present on all SeedViewer pages. The first link '''What is the SEED''' will lead you to the [[Home_of_the_SEED|SEED Homepage]]. Clicking the second link '''How to use the SEED Viewer''' will get you to this wiki. '''Submitting data to SEED''' lets you browse the [[RAST_Tutorial|RAST Tutorial]]. '''Contact''' enables you to write an email to the SEED team. Clicking '''Register''' is the first step to get a user account. It will lead to the [[SEED_Viewer_Manual/Register|Register]] page. '''I forgot my password''' enables you to [[SEED_Viewer_Manual/RequestNewPassword|Request a new password]]. [[Image:MenuHelp.png]] === Organism Menu === In the context of a selected organism, an organism menu will appear. '''General Information''' will lead to the [[SEED_Viewer_Manual/OrganismPage|Organism Page]] of the selected organism. The '''Feature Table''' will open the [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] and show you the features present in that organism. '''Genome Browser''' leads to the [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] for the selected organism. Clicking '''Scenarios''' shows the [[SEED_Viewer_Manual/Scenarios|Scenarios]] page for your organism. '''Subsystems''' opens a page that lets you select subsystems. '''Export''' enables you to [[SEED_Viewer_Manual/Export|download]] the features of your organism. [[Image:MenuOrganism.png]] === Comparative Tools === This menu is also present whenever an organism is viewed. Different kinds of comparisons of your selected organism to other organisms are available here. '''Function based Comparison''' - The [[SEED_Viewer_Manual/CompareMetabolicReconstruction|Compare Metabolic Reconstruction]] will enable you to see the metabolic reconstruction of your selected organism against that of another one. The '''Sequence based Comparison''' [[SEED_Viewer_Manual/MultiGenomeCompare|Multi Genome Compare]] shows a table and a graphics comparing a selected set of organisms projected against your chosen one (BLAST-based). Use the '''KEGG Metabolic Analysis''' [[SEED_Viewer_Manual/KEGG|to project the metabolic capabilities]] of your organism on KEGG maps. Blasting against your organism is enabled using the '''[[SEED_Viewer_Manual/BLASTOrganism|BLAST Search]]'''. [[Image:CompTools.png]] === Feature Menu === Whenever a feature is defined on a SeedViewer page, you will find the '''Feature''' menu for that feature. The '''Feature Overview''' points to the [[SEED_Viewer_Manual/Annotation|Annotation]] page. It shows general information about the feature, als well as a Compare Regions View that displays the feature in its genomic context and in comparison to homologs in other genomes. '''DNA Sequence''' will open a page with the DNA Sequence of the feature (in FASTA format). '''DNA w/ flanking''' not only prints the DNA sequence of the feature, but also includes a user-defined number of bases upstream and downstream of the feature. '''Protein Sequence''' will show you the protein FASTA sequence (translated from the DNA sequence) of the feature. '''Feature Evidence vs. FIG''' and '''Feature Evidence vs. all DB''' link to the [[SEED_Viewer_Manual/Evidence|Evidence]] page. The difference between the two is that the evidence shown for the feature includes only evidence against features in the SEED or also against other databases (e.g. GenBank, SwissProt, UniProt and many others). The evidence page will also allow you to make this selection or change it there. [[Image:MenuFeature.png]] === Feature Tools === This menu is also present if a feature is defined. It lets the user run a variaty of tools using the feature sequence. These include tools that look for transmembrane helices (e.g. [http://www.cbs.dtu.dk/services/TMHMM/ TMHMM]), signal peptides ([http://www.psort.org/ PSORT], [http://www.cbs.dtu.dk/services/SignalP/ SignalP]), protein domains (e.g. [http://www.ebi.ac.uk/interpro/ InterPro], [http://prodom.prabi.fr/prodom/current/html/home.php ProDom]) and others. [[Image:MenuFeatTools.png]] === FIGfams Menu === On SeedViewer pages that deal with [[Glossary#FIGfam|FIGfams]], you will find an additional FIGfams menu. The '''Home''' link leads to the entry page to [[SEED_Viewer_Manual/FIGfams|FIGfams]]. The '''Release History''' will lead you to a [[SEED_Viewer_Manual/FIGfamsRelease|page]] containing a number of statistics about the current release of the FIGfams. '''Download''' will connect you to the FTP server to enable you to download the FIGfams. [[Image:MenuFIGfam.png]] fcd969de87868f502834dcd9144d8023e03b0d53 2311 2295 2008-12-03T18:21:03Z DanielaBartels 10 /* Navigate Menu */ wikitext text/x-wiki == Menu Overview == The menu is a small bar below the logo of each page. Most menus have submenus that can be accessed via hovering over the menu. Right-click the submenu you want to go to. If no submenu is present, you can directly click the menu itself. === Navigate Menu === This menu is present on every SeedViewer page. The first entry '''Startpage''' will lead to the SeedViewer [[SEED_Viewer_Manual|HomePage]]. '''Organisms''' will open the [[SEED_Viewer_Manual/OrganismSelect|Organism Select]] page. You will see an overview of all organisms in the SEED and are able to select one to view in detail. '''Subsystems''' will do the same for subsystems. '''Scenarios''' lets you browse [[Glossary#Scenarios|Scenarios]] on the [[SEED_Viewer_Manual/Scenarios|Scenarios Page]]. '''FIGFams''' leads to an entry point for browsing [[SEED_Viewer_Manual/FIGfams|FIGfams]]. You can find more information about FIGfams [[Glossary#FIGfam|here]]. The '''BLAST Search''' links to the [[SEED_Viewer_Manual/BLASTOrganism|BLAST Page]]. You will be able to BLAST a sequence against an organism in the SEED. [[Image:MenuNav.png]] === Help Menu === This menu is also present on all SeedViewer pages. The first link '''What is the SEED''' will lead you to the [[Home_of_the_SEED|SEED Homepage]]. Clicking the second link '''How to use the SEED Viewer''' will get you to this wiki. '''Submitting data to SEED''' lets you browse the [[RAST_Tutorial|RAST Tutorial]]. '''Contact''' enables you to write an email to the SEED team. Clicking '''Register''' is the first step to get a user account. It will lead to the [[SEED_Viewer_Manual/Register|Register]] page. '''I forgot my password''' enables you to [[SEED_Viewer_Manual/RequestNewPassword|Request a new password]]. [[Image:MenuHelp.png]] === Organism Menu === In the context of a selected organism, an organism menu will appear. '''General Information''' will lead to the [[SEED_Viewer_Manual/OrganismPage|Organism Page]] of the selected organism. The '''Feature Table''' will open the [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] and show you the features present in that organism. '''Genome Browser''' leads to the [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] for the selected organism. Clicking '''Scenarios''' shows the [[SEED_Viewer_Manual/Scenarios|Scenarios]] page for your organism. '''Subsystems''' opens a page that lets you select subsystems. '''Export''' enables you to [[SEED_Viewer_Manual/Export|download]] the features of your organism. [[Image:MenuOrganism.png]] === Comparative Tools === This menu is also present whenever an organism is viewed. Different kinds of comparisons of your selected organism to other organisms are available here. '''Function based Comparison''' - The [[SEED_Viewer_Manual/CompareMetabolicReconstruction|Compare Metabolic Reconstruction]] will enable you to see the metabolic reconstruction of your selected organism against that of another one. The '''Sequence based Comparison''' [[SEED_Viewer_Manual/MultiGenomeCompare|Multi Genome Compare]] shows a table and a graphics comparing a selected set of organisms projected against your chosen one (BLAST-based). Use the '''KEGG Metabolic Analysis''' [[SEED_Viewer_Manual/KEGG|to project the metabolic capabilities]] of your organism on KEGG maps. Blasting against your organism is enabled using the '''[[SEED_Viewer_Manual/BLASTOrganism|BLAST Search]]'''. [[Image:CompTools.png]] === Feature Menu === Whenever a feature is defined on a SeedViewer page, you will find the '''Feature''' menu for that feature. The '''Feature Overview''' points to the [[SEED_Viewer_Manual/Annotation|Annotation]] page. It shows general information about the feature, als well as a Compare Regions View that displays the feature in its genomic context and in comparison to homologs in other genomes. '''DNA Sequence''' will open a page with the DNA Sequence of the feature (in FASTA format). '''DNA w/ flanking''' not only prints the DNA sequence of the feature, but also includes a user-defined number of bases upstream and downstream of the feature. '''Protein Sequence''' will show you the protein FASTA sequence (translated from the DNA sequence) of the feature. '''Feature Evidence vs. FIG''' and '''Feature Evidence vs. all DB''' link to the [[SEED_Viewer_Manual/Evidence|Evidence]] page. The difference between the two is that the evidence shown for the feature includes only evidence against features in the SEED or also against other databases (e.g. GenBank, SwissProt, UniProt and many others). The evidence page will also allow you to make this selection or change it there. [[Image:MenuFeature.png]] === Feature Tools === This menu is also present if a feature is defined. It lets the user run a variaty of tools using the feature sequence. These include tools that look for transmembrane helices (e.g. [http://www.cbs.dtu.dk/services/TMHMM/ TMHMM]), signal peptides ([http://www.psort.org/ PSORT], [http://www.cbs.dtu.dk/services/SignalP/ SignalP]), protein domains (e.g. [http://www.ebi.ac.uk/interpro/ InterPro], [http://prodom.prabi.fr/prodom/current/html/home.php ProDom]) and others. [[Image:MenuFeatTools.png]] === FIGfams Menu === On SeedViewer pages that deal with [[Glossary#FIGfam|FIGfams]], you will find an additional FIGfams menu. The '''Home''' link leads to the entry page to [[SEED_Viewer_Manual/FIGfams|FIGfams]]. The '''Release History''' will lead you to a [[SEED_Viewer_Manual/FIGfamsRelease|page]] containing a number of statistics about the current release of the FIGfams. '''Download''' will connect you to the FTP server to enable you to download the FIGfams. [[Image:MenuFIGfam.png]] b0bf8bd38a5f1fc7a515857deb8a9fd317061c9e 2313 2311 2008-12-03T18:31:15Z DanielaBartels 10 /* Navigate Menu */ wikitext text/x-wiki == Menu Overview == The menu is a small bar below the logo of each page. Most menus have submenus that can be accessed via hovering over the menu. Right-click the submenu you want to go to. If no submenu is present, you can directly click the menu itself. === Navigate Menu === This menu is present on every SeedViewer page. The first entry '''Startpage''' will lead to the SeedViewer [[SEED_Viewer_Manual|HomePage]]. '''Organisms''' will open the [[SEED_Viewer_Manual/OrganismSelect|Organism Select]] page. You will see an overview of all organisms in the SEED and are able to select one to view in detail. '''Subsystems''' will do the same for subsystems. '''Scenarios''' lets you browse [[Glossary#Scenarios|Scenarios]] on the [[SEED_Viewer_Manual/Scenarios|Scenarios Page]]. '''FIGFams''' leads to an entry point for browsing [[SEED_Viewer_Manual/FIGfamViewer|FIGfams]]. You can find more information about FIGfams [[Glossary#FIGfam|here]]. The '''BLAST Search''' links to the [[SEED_Viewer_Manual/BLASTOrganism|BLAST Page]]. You will be able to BLAST a sequence against an organism in the SEED. [[Image:MenuNav.png]] === Help Menu === This menu is also present on all SeedViewer pages. The first link '''What is the SEED''' will lead you to the [[Home_of_the_SEED|SEED Homepage]]. Clicking the second link '''How to use the SEED Viewer''' will get you to this wiki. '''Submitting data to SEED''' lets you browse the [[RAST_Tutorial|RAST Tutorial]]. '''Contact''' enables you to write an email to the SEED team. Clicking '''Register''' is the first step to get a user account. It will lead to the [[SEED_Viewer_Manual/Register|Register]] page. '''I forgot my password''' enables you to [[SEED_Viewer_Manual/RequestNewPassword|Request a new password]]. [[Image:MenuHelp.png]] === Organism Menu === In the context of a selected organism, an organism menu will appear. '''General Information''' will lead to the [[SEED_Viewer_Manual/OrganismPage|Organism Page]] of the selected organism. The '''Feature Table''' will open the [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] and show you the features present in that organism. '''Genome Browser''' leads to the [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] for the selected organism. Clicking '''Scenarios''' shows the [[SEED_Viewer_Manual/Scenarios|Scenarios]] page for your organism. '''Subsystems''' opens a page that lets you select subsystems. '''Export''' enables you to [[SEED_Viewer_Manual/Export|download]] the features of your organism. [[Image:MenuOrganism.png]] === Comparative Tools === This menu is also present whenever an organism is viewed. Different kinds of comparisons of your selected organism to other organisms are available here. '''Function based Comparison''' - The [[SEED_Viewer_Manual/CompareMetabolicReconstruction|Compare Metabolic Reconstruction]] will enable you to see the metabolic reconstruction of your selected organism against that of another one. The '''Sequence based Comparison''' [[SEED_Viewer_Manual/MultiGenomeCompare|Multi Genome Compare]] shows a table and a graphics comparing a selected set of organisms projected against your chosen one (BLAST-based). Use the '''KEGG Metabolic Analysis''' [[SEED_Viewer_Manual/KEGG|to project the metabolic capabilities]] of your organism on KEGG maps. Blasting against your organism is enabled using the '''[[SEED_Viewer_Manual/BLASTOrganism|BLAST Search]]'''. [[Image:CompTools.png]] === Feature Menu === Whenever a feature is defined on a SeedViewer page, you will find the '''Feature''' menu for that feature. The '''Feature Overview''' points to the [[SEED_Viewer_Manual/Annotation|Annotation]] page. It shows general information about the feature, als well as a Compare Regions View that displays the feature in its genomic context and in comparison to homologs in other genomes. '''DNA Sequence''' will open a page with the DNA Sequence of the feature (in FASTA format). '''DNA w/ flanking''' not only prints the DNA sequence of the feature, but also includes a user-defined number of bases upstream and downstream of the feature. '''Protein Sequence''' will show you the protein FASTA sequence (translated from the DNA sequence) of the feature. '''Feature Evidence vs. FIG''' and '''Feature Evidence vs. all DB''' link to the [[SEED_Viewer_Manual/Evidence|Evidence]] page. The difference between the two is that the evidence shown for the feature includes only evidence against features in the SEED or also against other databases (e.g. GenBank, SwissProt, UniProt and many others). The evidence page will also allow you to make this selection or change it there. [[Image:MenuFeature.png]] === Feature Tools === This menu is also present if a feature is defined. It lets the user run a variaty of tools using the feature sequence. These include tools that look for transmembrane helices (e.g. [http://www.cbs.dtu.dk/services/TMHMM/ TMHMM]), signal peptides ([http://www.psort.org/ PSORT], [http://www.cbs.dtu.dk/services/SignalP/ SignalP]), protein domains (e.g. [http://www.ebi.ac.uk/interpro/ InterPro], [http://prodom.prabi.fr/prodom/current/html/home.php ProDom]) and others. [[Image:MenuFeatTools.png]] === FIGfams Menu === On SeedViewer pages that deal with [[Glossary#FIGfam|FIGfams]], you will find an additional FIGfams menu. The '''Home''' link leads to the entry page to [[SEED_Viewer_Manual/FIGfams|FIGfams]]. The '''Release History''' will lead you to a [[SEED_Viewer_Manual/FIGfamsRelease|page]] containing a number of statistics about the current release of the FIGfams. '''Download''' will connect you to the FTP server to enable you to download the FIGfams. [[Image:MenuFIGfam.png]] b6977421e0c369fb1a31abcb148e5744bf98d570 2315 2313 2008-12-03T18:33:10Z DanielaBartels 10 /* Navigate Menu */ wikitext text/x-wiki == Menu Overview == The menu is a small bar below the logo of each page. Most menus have submenus that can be accessed via hovering over the menu. Right-click the submenu you want to go to. If no submenu is present, you can directly click the menu itself. === Navigate Menu === This menu is present on every SeedViewer page. The first entry '''Startpage''' will lead to the SeedViewer [[SEED_Viewer_Manual|HomePage]]. '''Organisms''' will open the [[SEED_Viewer_Manual/OrganismSelect|Organism Select]] page. You will see an overview of all organisms in the SEED and are able to select one to view in detail. '''Subsystems''' will do the same for subsystems. '''Scenarios''' lets you browse [[Glossary#Scenarios|Scenarios]] on the [[SEED_Viewer_Manual/Scenarios|Scenarios Page]]. '''FIGFams''' leads to an entry point for browsing [[SEED_Viewer_Manual/FIGfams|FIGfams]]. You can find more information about FIGfams [[Glossary#FIGfam|here]]. The '''BLAST Search''' links to the [[SEED_Viewer_Manual/BLASTOrganism|BLAST Page]]. You will be able to BLAST a sequence against an organism in the SEED. [[Image:MenuNav.png]] === Help Menu === This menu is also present on all SeedViewer pages. The first link '''What is the SEED''' will lead you to the [[Home_of_the_SEED|SEED Homepage]]. Clicking the second link '''How to use the SEED Viewer''' will get you to this wiki. '''Submitting data to SEED''' lets you browse the [[RAST_Tutorial|RAST Tutorial]]. '''Contact''' enables you to write an email to the SEED team. Clicking '''Register''' is the first step to get a user account. It will lead to the [[SEED_Viewer_Manual/Register|Register]] page. '''I forgot my password''' enables you to [[SEED_Viewer_Manual/RequestNewPassword|Request a new password]]. [[Image:MenuHelp.png]] === Organism Menu === In the context of a selected organism, an organism menu will appear. '''General Information''' will lead to the [[SEED_Viewer_Manual/OrganismPage|Organism Page]] of the selected organism. The '''Feature Table''' will open the [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] and show you the features present in that organism. '''Genome Browser''' leads to the [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] for the selected organism. Clicking '''Scenarios''' shows the [[SEED_Viewer_Manual/Scenarios|Scenarios]] page for your organism. '''Subsystems''' opens a page that lets you select subsystems. '''Export''' enables you to [[SEED_Viewer_Manual/Export|download]] the features of your organism. [[Image:MenuOrganism.png]] === Comparative Tools === This menu is also present whenever an organism is viewed. Different kinds of comparisons of your selected organism to other organisms are available here. '''Function based Comparison''' - The [[SEED_Viewer_Manual/CompareMetabolicReconstruction|Compare Metabolic Reconstruction]] will enable you to see the metabolic reconstruction of your selected organism against that of another one. The '''Sequence based Comparison''' [[SEED_Viewer_Manual/MultiGenomeCompare|Multi Genome Compare]] shows a table and a graphics comparing a selected set of organisms projected against your chosen one (BLAST-based). Use the '''KEGG Metabolic Analysis''' [[SEED_Viewer_Manual/KEGG|to project the metabolic capabilities]] of your organism on KEGG maps. Blasting against your organism is enabled using the '''[[SEED_Viewer_Manual/BLASTOrganism|BLAST Search]]'''. [[Image:CompTools.png]] === Feature Menu === Whenever a feature is defined on a SeedViewer page, you will find the '''Feature''' menu for that feature. The '''Feature Overview''' points to the [[SEED_Viewer_Manual/Annotation|Annotation]] page. It shows general information about the feature, als well as a Compare Regions View that displays the feature in its genomic context and in comparison to homologs in other genomes. '''DNA Sequence''' will open a page with the DNA Sequence of the feature (in FASTA format). '''DNA w/ flanking''' not only prints the DNA sequence of the feature, but also includes a user-defined number of bases upstream and downstream of the feature. '''Protein Sequence''' will show you the protein FASTA sequence (translated from the DNA sequence) of the feature. '''Feature Evidence vs. FIG''' and '''Feature Evidence vs. all DB''' link to the [[SEED_Viewer_Manual/Evidence|Evidence]] page. The difference between the two is that the evidence shown for the feature includes only evidence against features in the SEED or also against other databases (e.g. GenBank, SwissProt, UniProt and many others). The evidence page will also allow you to make this selection or change it there. [[Image:MenuFeature.png]] === Feature Tools === This menu is also present if a feature is defined. It lets the user run a variaty of tools using the feature sequence. These include tools that look for transmembrane helices (e.g. [http://www.cbs.dtu.dk/services/TMHMM/ TMHMM]), signal peptides ([http://www.psort.org/ PSORT], [http://www.cbs.dtu.dk/services/SignalP/ SignalP]), protein domains (e.g. [http://www.ebi.ac.uk/interpro/ InterPro], [http://prodom.prabi.fr/prodom/current/html/home.php ProDom]) and others. [[Image:MenuFeatTools.png]] === FIGfams Menu === On SeedViewer pages that deal with [[Glossary#FIGfam|FIGfams]], you will find an additional FIGfams menu. The '''Home''' link leads to the entry page to [[SEED_Viewer_Manual/FIGfams|FIGfams]]. The '''Release History''' will lead you to a [[SEED_Viewer_Manual/FIGfamsRelease|page]] containing a number of statistics about the current release of the FIGfams. '''Download''' will connect you to the FTP server to enable you to download the FIGfams. [[Image:MenuFIGfam.png]] b0bf8bd38a5f1fc7a515857deb8a9fd317061c9e 0 1576 2296 2008-12-03T16:45:40Z DanielaBartels 10 wikitext text/x-wiki == Scenarios == [[Image:Scenarios1.png]] [[Image:Scenarios2.png]] 0761fbdf65ed4e2060b5d90de82d6466ef770dd1 2299 2296 2008-12-03T16:49:56Z DanielaBartels 10 /* Scenarios */ wikitext text/x-wiki == Scenarios == [[Glossary#Scenarios]] [[Image:Scenarios1.png]] [[Image:Scenarios2.png]] 8e6da7997a6f3afe62b8234bd071bc9088c256a2 2301 2299 2008-12-03T16:54:43Z DanielaBartels 10 /* Scenarios */ wikitext text/x-wiki == Scenarios == [[Glossary#Scenarios|Scenarios]] are components of a metabolic reaction network in which specific compounds are labeled as inputs and outputs. The [[WebComponents/Table|table]] on this page lists all Scenarios. You can select a number of genomes to find out which scenarios are present for these organisms. [[Image:Scenarios1.png]] [[Image:Scenarios2.png]] d3e5d5bf9e41e2995dd3eba337723bb1b3e1d8e9 2302 2301 2008-12-03T17:59:59Z DanielaBartels 10 /* Scenarios */ wikitext text/x-wiki == Scenarios == [[Glossary#Scenarios|Scenarios]] are components of a metabolic reaction network in which specific compounds are labeled as inputs and outputs. The [[WebComponents/Table|table]] on this page lists all Scenarios. You can select a number of genomes to find out which scenarios are present for these organisms. To choose the organisms of interest, you can click the button '''select organisms'''. It will open a [[WebComponents/ListSelect|List Select]] that contains all organisms you can choose from. Select an organism and press the right arrow. The organism will appear in the right box and the table will be updated. An additional column will appear for the chosen organism. [[Image:Scenarios1.png]] [[Image:Scenarios2.png]] 44e40e6033a3bf33dd4662ba82569d5350d10dbb 2303 2302 2008-12-03T18:09:00Z DanielaBartels 10 /* Scenarios */ wikitext text/x-wiki == Scenarios == [[Glossary#Scenarios|Scenarios]] are components of a metabolic reaction network in which specific compounds are labeled as inputs and outputs. The [[WebComponents/Table|table]] on this page lists all Scenarios. You can select a number of genomes to find out which scenarios are present for these organisms. To choose the organisms of interest, you can click the button '''select organisms'''. It will open a [[WebComponents/ListSelect|List Select]] that contains all organisms you can choose from. Select an organism and press the right arrow. The organism will appear in the right box and the table will be updated. An additional column will appear for the chosen organism. [[Image:Scenarios1.png]] As a scenario is bound to a SEED [[Glossary#Subsystem|subsystem]], the first three columns show the classification ('''Category''' and '''Subcategory''') and the name of the '''Subsystem'''. The subsystem name links to its [[SEED_Viewer_Manual/Subsystem|Subsystem]] page. The name of the '''Scenario''' is displayed in the fourth column. The [[Image:Scenarios2.png]] dc4c6d15b616960165714dc6b0a301fb9d827f67 2305 2303 2008-12-03T18:10:45Z DanielaBartels 10 /* Scenarios */ wikitext text/x-wiki == Scenarios == [[Glossary#Scenarios|Scenarios]] are components of a metabolic reaction network in which specific compounds are labeled as inputs and outputs. The [[WebComponents/Table|table]] on this page lists all Scenarios. You can select a number of genomes to find out which scenarios are present for these organisms. To choose the organisms of interest, you can click the button '''select organisms'''. It will open a [[WebComponents/ListSelect|List Select]] that contains all organisms you can choose from. Select an organism and press the right arrow. The organism will appear in the right box and the table will be updated. An additional column will appear for the chosen organism. [[Image:Scenarios1.png]] As a scenario is bound to a SEED [[Glossary#Subsystems|subsystem]], the first three columns show the classification ('''Category''' and '''Subcategory''') and the name of the '''Subsystem'''. The subsystem name links to its [[SEED_Viewer_Manual/Subsystem|Subsystem]] page. The name of the '''Scenario''' is displayed in the fourth column. The [http://www.genome.jp/kegg/ KEGG] map for the scenario is shown in the next column. Following columns tell you for each chosen genome if the scenario is implemented in the organism. [[Image:Scenarios2.png]] 98890e689a89a0c09c175065d9b496158008fc48 2306 2305 2008-12-03T18:11:18Z DanielaBartels 10 /* Scenarios */ wikitext text/x-wiki == Scenarios == [[Glossary#Scenarios|Scenarios]] are components of a metabolic reaction network in which specific compounds are labeled as inputs and outputs. The [[WebComponents/Table|table]] on this page lists all Scenarios. You can select a number of genomes to find out which scenarios are present for these organisms. To choose the organisms of interest, you can click the button '''select organisms'''. It will open a [[WebComponents/ListSelect|List Select]] that contains all organisms you can choose from. Select an organism and press the right arrow. The organism will appear in the right box and the table will be updated. An additional column will appear for the chosen organism. [[Image:Scenarios1.png]] As a scenario is bound to a SEED [[Glossary#Subsystem|subsystem]], the first three columns show the classification ('''Category''' and '''Subcategory''') and the name of the '''Subsystem'''. The subsystem name links to its [[SEED_Viewer_Manual/Subsystems|Subsystem]] page. The name of the '''Scenario''' is displayed in the fourth column. The [http://www.genome.jp/kegg/ KEGG] map for the scenario is shown in the next column. Following columns tell you for each chosen genome if the scenario is implemented in the organism. [[Image:Scenarios2.png]] 26b99315e3cdf9f43238bcd2b4a4fcbdab751649 6 1577 2297 2008-12-03T16:45:53Z DanielaBartels 10 wikitext text/x-wiki da39a3ee5e6b4b0d3255bfef95601890afd80709 6 1578 2298 2008-12-03T16:46:09Z DanielaBartels 10 wikitext text/x-wiki da39a3ee5e6b4b0d3255bfef95601890afd80709 0 1367 2300 2162 2008-12-03T16:50:23Z DanielaBartels 10 /* RAST */ wikitext text/x-wiki === Aliases === Usually used in context of feature IDs. They are database crossreferences. === Annotators SEED === The master copy for all data in the SEED environment. Users can not access this password protected site. All annotations are made available via the [[#SEED-Viewer| SEED-Viewer]] and the [[#Trial-SEED|Trial-SEED]]. === Annotation === please see [[#Assigning_a_gene_function_and_annotation| Assigning a gene function and annotation]] === Assigning a gene function and annotation === Annotators assign gene functions to genes, and we call this process annotation. In most contexts, people use the term annotation to refer to assignments of function to the genes within a single organism. We certainly use the term in this sense, but we also use it to describe the process of assigning functions to corresponding genes from numerous genomes. Our basic approach to annotation is to ask our annotators to annotate the genes included in a [[#subsystem|Subsystem]] (e.g., glycolysis) across all genomes. This process of annotation of the genes within a subsystem across a set of genomes, rather than annotation of genes within a single genome, allows our annotators to focus on a constrained set of functional roles and attempt to accurately identify exactly what variant, if any, of a subsystem exists in each of the genomes. We use the term annotation to refer to assigning functions to genes (either within a single organism or to a constrained set of gene/protein families across a set of organisms). This activity certainly is closely related to the construction of subsystems and protein families (which we call FIGfams), but we will describe those activities elsewhere. === Assignment === please see [[#Assigning_a_gene_function_and_annotation| Assigning a gene function and annotation]] === Bidirectional Best Hit (BBH) === The paper [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=EBI&pubmedid=10077608 The use of gene clusters to infer functional coupling] defines a Bidirectional Best Hit or BBH as follows: <blockquote> Given two genes Xa and Xb from two genomes Ga and Gb, Xa and Xb are called a “bidirectional best hit (BBH)” if and only if recognizable similarity exists between them (in our case, we required fasta3 scores lower than 1.0 × 10−5), there is no gene Zb in Gb that is more similar than Xb is to Xa, and there is no gene Za in Ga that is more similar than Xa is to Xb. Genes (Xa, Ya) from Ga and (Xb, Yb) from Gb form a “pair of close bidirectional best hits (PCBBH)” if and only if Xa and Ya are close, Xb and Yb are close, Xa and Xb are a BBH, and Ya and Yb are a BBH. </blockquote> === Clearinghouse === please see [[#SubsystemClearinghouse|Subsystem Clearinghouse]] ===Feature=== A feature is a defined region in the DNA. A PEG is the most prevalent feature type in the SEED. Some other feature types include RNA, prophage and pathogenicity islands. The format for a feature ID is fig|genome_id.feature_abbreviation.feature_number (ie fig|83333.1.peg.100 ). === FIGfam === FIGfams are protein families generated by the Fellowship for Interpretation of Genomes (FIG). These families are based on the collection of subsystems, as well as correspondences between genes in closely related strains (we describe the construction of FIGfams in a separate SOP). The important properties of these families are as follows: # Two PEGs which both occur within a single FIGfam are believed to have the same function. # There is a decision procedure associated with the family which can be invoked to determine whether or not a gene can be “safely” assigned the function associated with the family. === FIG Identifier / FIG-IDs === We provide identifiers for genome sequences and features in the following form: {| ! Entity type !! key !! identifier |- | Genome || genome || fig<nowiki>|</nowiki>83331.1 |- | PEG || id || fig<nowiki>|</nowiki>83331.peg.123 |- | RNA feature || id || fig<nowiki>|</nowiki>83331.rna.1 |- |} (Please also see below for information on how to link to the SEED.) === Functional coupling === The availability of multiple genomes provides an opportunity to gain new insights into the processes that drive the dispersion and formation of chromosomal gene clusters. The paper [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=EBI&pubmedid=10077608 The use of gene clusters to infer functional coupling] describes a method to compute functional coupling of features due to conserved gene clusters . === Functional role === The concept of functional role is both basic and primitive in the sense that we will not pretend to offer a precise definition. It corresponds roughly to a single logical role that a gene or gene product may play in the operation of a cell. === Gene function === The function of a protein-encoding gene (PEG) is the functional role played by the product of the gene or an expression describing a set of roles played by the encoded protein. The operators used to construct expressions and the meanings associated with the operators are described in http://www.nmpdr.org/FIG/Html/SEED_functions.html Genes other than PEGs can also be assigned functions (e.g., SSU rRNA). However, in most cases the functions assigned to genes other than PEGs tend not to be problematic. === Linking to the SEED === We support linking to the SEED using a generic mechanism: Base URL: http://www.theseed.org/linkin.cgi? {| |+ Supported SEED Identifiers for external use ! Entity type !! key !! identifier !! Example |- | Genome || genome || fig<nowiki>|</nowiki>83331.1 || [[http://www.theseed.org/linkin.cgi?genome=fig|83333.1 http://www.theseed.org/linkin.cgi?genome=fig&#124;83333.1]] |- | PEG || id || fig<nowiki>|</nowiki>83331.peg.123 || [[http://www.theseed.org/linkin.cgi?id=fig|83333.1.peg.123 http://www.theseed.org/linkin.cgi?id=fig&#124;83333.1.peg.123]] |- | RNA feature || id || fig<nowiki>|</nowiki>83331.rna.1 || [[http://www.theseed.org/linkin.cgi?id=fig|83333.1.rna.1 http://www.theseed.org/linkin.cgi?id=fig&#124;83333.1.rna.1]] |- |} SEED identifiers contain the NCBI taxonomy ID, thus if the taxonomy ID changes, we need to update our internal data accordingly. To provide stable external identifiers, we keep a list of IDs that have changed and display warning message informing the user of the change and provide a link to the new version of the data requested. === Metabolic Reconstruction === When we use the term metabolic reconstruction of a given genome we will simply mean the set of populated subsystems that contain the genome, the PEGs (and their assigned functions) that are connected to functional roles in these populated subsystems, and the specific variant code associated with the genome in each of the populated subsystems. === NMPDR pathogen genome === The NMPDR is responsible for five classes of genomes: # Campylobacter jejuni # Listeria monocytogenes # Staphylococcus aureus # Streptococcus pneumoniae and Streptococcus pyogenes # Pathogenic Vibrio === Pair of Close Homologs (PCH) === The paper [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=EBI&pubmedid=10077608 The use of gene clusters to infer functional coupling] defines a Pair of Close Homologs as follows: <blockquote> We can also define the concept of “pairs of close homologs” (PCHs) as follows: genes (X′a, Y′a) from Ga and (X′b, Y′b) from Gb form a PCH if and only if X′a and Y′a are close, X′b and Y′b are close, X′a and X′b are recognizably similar, and Y′a and Y′b are recognizably similar. Here, we will consider two genes to be recognizably similar if their gene products produce fasta3 scores lower than 1.0 × 10−5. We use a scoring scheme analogous to the one described for PCBBHs to evaluate the connections between PCHs, except that if Ga and Gb are the same genome, we assign an arbitrary “same-genome score” (“same-genome” pairs cannot occur for PCBBHs by definition, but for PCHs they are possible). Unlike PCBBHs from two very close genomes for which contiguity is completely uninformative in the vast majority of cases, PCHs allow recognition of gene clusters that play similar (but usually not identical) roles (such as two transport cassettes containing pairs of homologs) in the same or similar organisms. The arbitrary “same-genome score” should, we believe, have a value that is high enough to rank such instances as significant. </blockquote> === PEG === A Protein Encoding Gene (PEG) is equivalent to a CDS (Coding Sequence). === Populated Subsystem === please see [[#Subsystem|Subsystem]] === RAST === RAST or Rapid Annotation using Subsystem Technology is a rapid and very accurate annotation technology. We make a RAST server available for public use at http://rast.nmpdr.org === Scenarios === Scenarios represent components of a metabolic reaction network in which specific compounds are labeled as inputs and outputs. The metabolic network is assembled using biochemical reaction information associated with functional roles in subsystems to find paths through scenarios from inputs to outputs. Scenarios that are connected by linked inputs and outputs can be composed to form larger blocks of the metabolic network, spanning processes that convert transported nutrients into biomass components. === SEED-Viewer === The SEED Viewer is a web-based application that allows browsing of SEED data structures. We use the SEED-Viewer to provide a public read-only version of the latest SEED data at: http://seed-viewer.theseed.org '''Please note''': The data is updated automatically every 24 hours. When citing or linking to the SEED please use this version. === Subsystem === A subsystem is a set of functional roles that an annotator has decided should be thought of as related. Frequently, subsystems represent the collection of [[#Functional_role|functional roles]] that make up a metabolic pathway, a complex (e.g., the ribosome), or a class of proteins (e.g., two-component signal-transduction proteins within Staphylococcus aureus). A '''populated subsystem''' is a subsystem with an attached spreadsheet. The rows of the spreadsheet represent genomes and the columns represent the functional roles of the spreadsheet. Each cell contains the identifiers of genes from the corresponding genome the implement the specific functional role. That is, a populated subsystem specifies which genes implement instances of the subsystem in each of the genomes. The rows of a populated genome are assigned '''variant codes''' which describe which of a set of possible variants of the subsystem exist within each genome (special codes expressing a total absence of the subsystem or remaining uncertainty exist). Construction of a large set of curated populated subsystems is at the center of the NMPDR and SEED annotation efforts. === Subsystem Clearing House === Since annotators can work on any machine (including the public SEED) the way to propagate subsystems is via http://clearinghouse.theseed.org/clearinghouse_browser.cgi? === Trial-SEED === A public, read-write copy of the SEED is made available on http://theseed.uchicago.edu/FIG/index.cgi '''Please note''': The data on this server is updated in irregular intervals. Users should not assume that annotations made on this system will persist. Please publish your annotations to the [[#Subsystem_clearing_house|Subsystem Clearing house]]. === Variant Code=== please see [[#Subsystem|Subsystem]] 424d1ce0446d7556e9f397cf5f380017f0c4f09d 0 1517 2304 2187 2008-12-03T18:09:49Z TobiasPaczian 17 /* Subsystems */ wikitext text/x-wiki == Subsystems == A [[Glossary#Subsystem|subsystem]] is a collection of [[Glossary#Functional role|functional roles]] that are associated to each other in a system. Such a system can for example be a metabolic pathway or a component of a cell like a secretion system. The subsystem page in the SeedViewer is divided into different parts via a [[WebComponents/Tabview|TabView]]. The TabView can consist of 3-5 tabs. The first tab shows a '''Diagram''' of the subsystem, the second tab displays a [[WebComponents/Table|table]] with the '''Functional Roles''' present in the subsystem. The '''Spreadsheet''' relating the functional roles in the subsystem to features in genomes can be found in the third tab. The fourth and fifth tab show a description and additional notes to a subsystem. They only appear if a subsystem has a description / notes. === Diagram === The subsystem diagram shows the connections between the functional roles in a subsystem. The boxes represent the functional roles via their abbreviations. The circles are connecting intermediates, that are described in the table which is part of the diagram. The functional roles in the diagram can be colored according to their presence in a genome. Click the button '''Color Diagram''' to get a combo box with all genomes in the subsystem. Select your genome of interest and press '''do coloring'''. The boxes for the functional roles defined for that genome will now be colored in green. [[Image:SubsystemDiagram.png]] === Functional Roles === This [[WebComponents/Table|table]] lists all functional roles present in the subsystem. The first column shows '''Group Aliases''' for the functional role. Functional roles can be aggregated in groups (subsets). Subset names that start with a '*' contain alternative ways to implement a function. The abbreviation ('''Abbrev.''') for a functional role must be unique for the functional roles in the subsystem. They are used in different displays like the Diagram or the Speadsheet. The third column lists the full name of the functional role. EC-Numbers are often part of the functional role (for enzymes), and are stated in parentheses after the name of the functional role. The following two columns deal with reactions a functional role is connected to. Clicking on the link opens a new window showing the KEGG reaction. Next to annotator-curated KEGG reactions, we show the KEGG reactions of the curation effort of the [[SEED_People#Hope College|Hope College]] team that collaborates with the SEED. GeneOntology (GO) links are displayed in the next column. The links point to the GO-number in GeneOntology's Amigo-Tool. The last column can contain literature (PubMed IDs) that describes the functional role in detail. If present, you will find a link to PubMed in this column. [[Image:SubsystemFRs.png]] === Spreadsheet === The subsystem spreadsheet displays the features that are assigned with the functional roles in all organisms that are part of the subsystem. The organisms are displayed in the first column. The links lead to the [[SEED_Viewer_Manual/OrganismPage|Organism Page]]. The column header includes a filter option for the organism, doing an infix search on the organism name. The '''Domain''' (Bacterial, Archaeal or Eukaryote) of the organism is shown in the second column. For each organism in the spreadsheet, a '''Variant Code''' is assigned. Usually, there is more than one way to fulfill a subsystem. Metabolic pathways can have alternatives, or parts of the pathway may be present or absent in an organism. [[[Glossary/Variant Code|Variant Codes]] are assigned to the organism to express this behavior. There are two special Variant Codes: '''0''' and '''-1'''. The Variant Code '''-1''' means that the organism has no active variant in this subsystem, meaning it does not implement the subsystem. '''0''' means that the curator has not yet assigned a variant to the genome. Due to the flow of newly sequenced genomes into the SEED, this variant code may show up sometimes. The next column is used to filter active or not active variants. If you want to see only the active ones (default), print '''yes''' into the filter in the column header. For seeing only the not active ones, print '''no'''. No input in this field will show all variants. All following columns in the table show the features in the organisms that are assigned with functional roles. The column headers display the abbreviations of the functional roles (see Functional Roles Table) Hovering over a column header will show a tooltip with the full name of the role. The feature entries in the cells for the functional roles are linked to the [[SEED_Viewer_Manual/Annotation|Annotation Page]] for that feature. There can be multiple features in a cell, as some functions are implemented by more that one feature in an organism. The control table on top of the spreadsheet table lets you change the display in the table: Functional Roles that belong to a subset starting with a '*', meaning they are alternatives for a function, are collapsed in the spreadsheet by default. If you want to expand the subsets, you can do so by checking '''expanded''' in the '''Subsets''' column. The feature entries in the spreadsheet can be colored according to different metaphors using the second column ('''Coloring''') of the table. By default, the features are colored '''by cluster'''. In this case, it is computed which features are close by on the genomic sequence, meaning they cluster. Each computed cluster gets its own color. These colors only have a meaning per genome, meaning that a yellow cluster in one genome has no connection to a yellow cluster in the next genome. Another way to cluster the features are different kinds of attributes. Check the radio box for '''by attribute''' and choose an attribute in the drop down menu. Press '''update''' to change the display. [[Image:SubsystemSpreadsheet.png]] === Description === The description of a subsystem gives an overview of the functional roles and their connections in the subsystem. It can give some background information about the system, what organisms it is usually found in and other facts that are of interest. === Additional Notes === As the description already gives an overview over the subsystem, additional notes can be found here. The notes usually refer to specific properties of some organisms or organism groups, genes that are missing but should be there and other details that might be useful for the interested user. d1572f0a59afc96364ada0451cb89fae0d773855 2307 2304 2008-12-03T18:16:04Z TobiasPaczian 17 /* Functional Roles */ wikitext text/x-wiki == Subsystems == A [[Glossary#Subsystem|subsystem]] is a collection of [[Glossary#Functional role|functional roles]] that are associated to each other in a system. Such a system can for example be a metabolic pathway or a component of a cell like a secretion system. The subsystem page in the SeedViewer is divided into different parts via a [[WebComponents/Tabview|TabView]]. The TabView can consist of 3-5 tabs. The first tab shows a '''Diagram''' of the subsystem, the second tab displays a [[WebComponents/Table|table]] with the '''Functional Roles''' present in the subsystem. The '''Spreadsheet''' relating the functional roles in the subsystem to features in genomes can be found in the third tab. The fourth and fifth tab show a description and additional notes to a subsystem. They only appear if a subsystem has a description / notes. === Diagram === The subsystem diagram shows the connections between the functional roles in a subsystem. The boxes represent the functional roles via their abbreviations. The circles are connecting intermediates, that are described in the table which is part of the diagram. The functional roles in the diagram can be colored according to their presence in a genome. Click the button '''Color Diagram''' to get a combo box with all genomes in the subsystem. Select your genome of interest and press '''do coloring'''. The boxes for the functional roles defined for that genome will now be colored in green. [[Image:SubsystemDiagram.png]] === Functional Roles === This [[WebComponents/Table|table]] lists all functional roles present in the subsystem. The first column shows '''Group Aliases''' for the functional role. Functional roles can be aggregated in groups (subsets). Subset names that start with a '*' contain alternative ways to implement a function. The abbreviation ('''Abbrev.''') for a functional role must be unique for the functional roles in the subsystem. It is used in different displays like the Diagram or the Speadsheet. The third column lists the full name of the functional role. EC-Numbers are often part of the functional role (for enzymes), and are stated in parentheses after the name of the functional role. The following two columns deal with reactions a functional role is connected to. Clicking on the link opens a new window showing the KEGG reaction. Next to annotator-curated KEGG reactions, we show the KEGG reactions of the curation effort of the [[SEED_People#Hope College|Hope College]] team that collaborates with the SEED. GeneOntology (GO) links are displayed in the next column. The links point to the GO-number in GeneOntology's Amigo-Tool. The last column can contain literature (PubMed IDs) that describes the functional role in detail. If present, you will find a link to PubMed in this column. [[Image:SubsystemFRs.png]] === Spreadsheet === The subsystem spreadsheet displays the features that are assigned with the functional roles in all organisms that are part of the subsystem. The organisms are displayed in the first column. The links lead to the [[SEED_Viewer_Manual/OrganismPage|Organism Page]]. The column header includes a filter option for the organism, doing an infix search on the organism name. The '''Domain''' (Bacterial, Archaeal or Eukaryote) of the organism is shown in the second column. For each organism in the spreadsheet, a '''Variant Code''' is assigned. Usually, there is more than one way to fulfill a subsystem. Metabolic pathways can have alternatives, or parts of the pathway may be present or absent in an organism. [[[Glossary/Variant Code|Variant Codes]] are assigned to the organism to express this behavior. There are two special Variant Codes: '''0''' and '''-1'''. The Variant Code '''-1''' means that the organism has no active variant in this subsystem, meaning it does not implement the subsystem. '''0''' means that the curator has not yet assigned a variant to the genome. Due to the flow of newly sequenced genomes into the SEED, this variant code may show up sometimes. The next column is used to filter active or not active variants. If you want to see only the active ones (default), print '''yes''' into the filter in the column header. For seeing only the not active ones, print '''no'''. No input in this field will show all variants. All following columns in the table show the features in the organisms that are assigned with functional roles. The column headers display the abbreviations of the functional roles (see Functional Roles Table) Hovering over a column header will show a tooltip with the full name of the role. The feature entries in the cells for the functional roles are linked to the [[SEED_Viewer_Manual/Annotation|Annotation Page]] for that feature. There can be multiple features in a cell, as some functions are implemented by more that one feature in an organism. The control table on top of the spreadsheet table lets you change the display in the table: Functional Roles that belong to a subset starting with a '*', meaning they are alternatives for a function, are collapsed in the spreadsheet by default. If you want to expand the subsets, you can do so by checking '''expanded''' in the '''Subsets''' column. The feature entries in the spreadsheet can be colored according to different metaphors using the second column ('''Coloring''') of the table. By default, the features are colored '''by cluster'''. In this case, it is computed which features are close by on the genomic sequence, meaning they cluster. Each computed cluster gets its own color. These colors only have a meaning per genome, meaning that a yellow cluster in one genome has no connection to a yellow cluster in the next genome. Another way to cluster the features are different kinds of attributes. Check the radio box for '''by attribute''' and choose an attribute in the drop down menu. Press '''update''' to change the display. [[Image:SubsystemSpreadsheet.png]] === Description === The description of a subsystem gives an overview of the functional roles and their connections in the subsystem. It can give some background information about the system, what organisms it is usually found in and other facts that are of interest. === Additional Notes === As the description already gives an overview over the subsystem, additional notes can be found here. The notes usually refer to specific properties of some organisms or organism groups, genes that are missing but should be there and other details that might be useful for the interested user. 0d0a649088b6196ecd78367a018edc1e0852e0fd 2308 2307 2008-12-03T18:17:45Z TobiasPaczian 17 /* Spreadsheet */ wikitext text/x-wiki == Subsystems == A [[Glossary#Subsystem|subsystem]] is a collection of [[Glossary#Functional role|functional roles]] that are associated to each other in a system. Such a system can for example be a metabolic pathway or a component of a cell like a secretion system. The subsystem page in the SeedViewer is divided into different parts via a [[WebComponents/Tabview|TabView]]. The TabView can consist of 3-5 tabs. The first tab shows a '''Diagram''' of the subsystem, the second tab displays a [[WebComponents/Table|table]] with the '''Functional Roles''' present in the subsystem. The '''Spreadsheet''' relating the functional roles in the subsystem to features in genomes can be found in the third tab. The fourth and fifth tab show a description and additional notes to a subsystem. They only appear if a subsystem has a description / notes. === Diagram === The subsystem diagram shows the connections between the functional roles in a subsystem. The boxes represent the functional roles via their abbreviations. The circles are connecting intermediates, that are described in the table which is part of the diagram. The functional roles in the diagram can be colored according to their presence in a genome. Click the button '''Color Diagram''' to get a combo box with all genomes in the subsystem. Select your genome of interest and press '''do coloring'''. The boxes for the functional roles defined for that genome will now be colored in green. [[Image:SubsystemDiagram.png]] === Functional Roles === This [[WebComponents/Table|table]] lists all functional roles present in the subsystem. The first column shows '''Group Aliases''' for the functional role. Functional roles can be aggregated in groups (subsets). Subset names that start with a '*' contain alternative ways to implement a function. The abbreviation ('''Abbrev.''') for a functional role must be unique for the functional roles in the subsystem. It is used in different displays like the Diagram or the Speadsheet. The third column lists the full name of the functional role. EC-Numbers are often part of the functional role (for enzymes), and are stated in parentheses after the name of the functional role. The following two columns deal with reactions a functional role is connected to. Clicking on the link opens a new window showing the KEGG reaction. Next to annotator-curated KEGG reactions, we show the KEGG reactions of the curation effort of the [[SEED_People#Hope College|Hope College]] team that collaborates with the SEED. GeneOntology (GO) links are displayed in the next column. The links point to the GO-number in GeneOntology's Amigo-Tool. The last column can contain literature (PubMed IDs) that describes the functional role in detail. If present, you will find a link to PubMed in this column. [[Image:SubsystemFRs.png]] === Spreadsheet === The subsystem spreadsheet displays the features that are assigned with the functional roles in all organisms that are part of the subsystem. The organisms are displayed in the first column. The links lead to the [[SEED_Viewer_Manual/OrganismPage|Organism Page]]. The column header includes a filter option for the organism, doing an infix search on the organism name. The '''Domain''' (Bacterial, Archaeal or Eukaryote) of the organism is shown in the second column. For each organism in the spreadsheet, a '''Variant Code''' is assigned. Usually, there is more than one way to fulfill a subsystem. Metabolic pathways can have alternatives, or parts of the pathway may be present or absent in an organism. [[Glossary/Variant Code|Variant Codes]] are assigned to the organism to express this behavior. There are two special Variant Codes: '''0''' and '''-1'''. The Variant Code '''-1''' means that the organism has no active variant in this subsystem, meaning it does not implement the subsystem. '''0''' means that the curator has not yet assigned a variant to the genome. Due to the flow of newly sequenced genomes into the SEED, this variant code may show up sometimes. The next column is used to filter active or not active variants. If you want to see only the active ones (default), print '''yes''' into the filter in the column header. For seeing only the not active ones, print '''no'''. No input in this field will show all variants. All following columns in the table show the features in the organisms that are assigned with functional roles. The column headers display the abbreviations of the functional roles (see Functional Roles Table) Hovering over a column header will show a tooltip with the full name of the role. The feature entries in the cells for the functional roles are linked to the [[SEED_Viewer_Manual/Annotation|Annotation Page]] for that feature. There can be multiple features in a cell, as some functions are implemented by more that one feature in an organism. The control table on top of the spreadsheet table lets you change the display in the table: Functional Roles that belong to a subset starting with a '*', meaning they are alternatives for a function, are collapsed in the spreadsheet by default. If you want to expand the subsets, you can do so by checking '''expanded''' in the '''Subsets''' column. The feature entries in the spreadsheet can be colored according to different metaphors using the second column ('''Coloring''') of the table. By default, the features are colored '''by cluster'''. In this case, it is computed which features are close by on the genomic sequence, meaning they cluster. Each computed cluster gets its own color. These colors only have a meaning per genome, meaning that a yellow cluster in one genome has no connection to a yellow cluster in the next genome. Another way to cluster the features are different kinds of attributes. Check the radio box for '''by attribute''' and choose an attribute in the drop down menu. Press '''update''' to change the display. [[Image:SubsystemSpreadsheet.png]] === Description === The description of a subsystem gives an overview of the functional roles and their connections in the subsystem. It can give some background information about the system, what organisms it is usually found in and other facts that are of interest. === Additional Notes === As the description already gives an overview over the subsystem, additional notes can be found here. The notes usually refer to specific properties of some organisms or organism groups, genes that are missing but should be there and other details that might be useful for the interested user. 1bfe8222507f6642a179e53f8cd3e8c301b22725 2309 2308 2008-12-03T18:19:53Z TobiasPaczian 17 /* Spreadsheet */ wikitext text/x-wiki == Subsystems == A [[Glossary#Subsystem|subsystem]] is a collection of [[Glossary#Functional role|functional roles]] that are associated to each other in a system. Such a system can for example be a metabolic pathway or a component of a cell like a secretion system. The subsystem page in the SeedViewer is divided into different parts via a [[WebComponents/Tabview|TabView]]. The TabView can consist of 3-5 tabs. The first tab shows a '''Diagram''' of the subsystem, the second tab displays a [[WebComponents/Table|table]] with the '''Functional Roles''' present in the subsystem. The '''Spreadsheet''' relating the functional roles in the subsystem to features in genomes can be found in the third tab. The fourth and fifth tab show a description and additional notes to a subsystem. They only appear if a subsystem has a description / notes. === Diagram === The subsystem diagram shows the connections between the functional roles in a subsystem. The boxes represent the functional roles via their abbreviations. The circles are connecting intermediates, that are described in the table which is part of the diagram. The functional roles in the diagram can be colored according to their presence in a genome. Click the button '''Color Diagram''' to get a combo box with all genomes in the subsystem. Select your genome of interest and press '''do coloring'''. The boxes for the functional roles defined for that genome will now be colored in green. [[Image:SubsystemDiagram.png]] === Functional Roles === This [[WebComponents/Table|table]] lists all functional roles present in the subsystem. The first column shows '''Group Aliases''' for the functional role. Functional roles can be aggregated in groups (subsets). Subset names that start with a '*' contain alternative ways to implement a function. The abbreviation ('''Abbrev.''') for a functional role must be unique for the functional roles in the subsystem. It is used in different displays like the Diagram or the Speadsheet. The third column lists the full name of the functional role. EC-Numbers are often part of the functional role (for enzymes), and are stated in parentheses after the name of the functional role. The following two columns deal with reactions a functional role is connected to. Clicking on the link opens a new window showing the KEGG reaction. Next to annotator-curated KEGG reactions, we show the KEGG reactions of the curation effort of the [[SEED_People#Hope College|Hope College]] team that collaborates with the SEED. GeneOntology (GO) links are displayed in the next column. The links point to the GO-number in GeneOntology's Amigo-Tool. The last column can contain literature (PubMed IDs) that describes the functional role in detail. If present, you will find a link to PubMed in this column. [[Image:SubsystemFRs.png]] === Spreadsheet === The subsystem spreadsheet displays the features that are assigned with the functional roles in all organisms that are part of the subsystem. The organisms are displayed in the first column. The links lead to the [[SEED_Viewer_Manual/OrganismPage|Organism Page]]. The column header includes a filter option for the organism, doing an infix search on the organism name. The '''Domain''' (Bacterial, Archaeal or Eukaryote) of the organism is shown in the second column. For each organism in the spreadsheet, a '''Variant Code''' is assigned. Usually, there is more than one way to fulfill a subsystem. Metabolic pathways can have alternatives, or parts of the pathway may be present or absent in an organism. [[Glossary/Variant Code|Variant Codes]] are assigned to the organism to express this behavior. There are two special Variant Codes: '''0''' and '''-1'''. The Variant Code '''-1''' means that the organism has no active variant in this subsystem, meaning it does not implement the subsystem. '''0''' means that the curator has not yet assigned a variant to the genome. Due to the flow of newly sequenced genomes into the SEED, this variant code may show up sometimes. The next column is used to filter active or inactive variants. If you want to see only the active ones (default), print '''yes''' into the filter in the column header. For seeing only the not active ones, print '''no'''. No input in this field will show all variants. All following columns in the table show the features in the organisms that are assigned with functional roles. The column headers display the abbreviations of the functional roles (see Functional Roles Table) Hovering over a column header will show a tooltip with the full name of the role. The feature entries in the cells for the functional roles are linked to the [[SEED_Viewer_Manual/Annotation|Annotation Page]] for that feature. There can be multiple features in a cell, as some functions are implemented by more that one feature in an organism. The control table on top of the spreadsheet table lets you change the display in the table: Functional Roles that belong to a subset starting with a '*', meaning they are alternatives for a function, are collapsed in the spreadsheet by default. If you want to expand the subsets, you can do so by checking '''expanded''' in the '''Subsets''' column. The feature entries in the spreadsheet can be colored according to different metaphors using the second column ('''Coloring''') of the table. By default, the features are colored '''by cluster'''. In this case, it is computed which features are close by on the genomic sequence, meaning they cluster. Each computed cluster gets its own color. These colors only have a meaning per genome, meaning that a yellow cluster in one genome has no connection to a yellow cluster in the next genome. Another way to cluster the features are different kinds of attributes. Check the radio box for '''by attribute''' and choose an attribute in the drop down menu. Press '''update''' to change the display. [[Image:SubsystemSpreadsheet.png]] === Description === The description of a subsystem gives an overview of the functional roles and their connections in the subsystem. It can give some background information about the system, what organisms it is usually found in and other facts that are of interest. === Additional Notes === As the description already gives an overview over the subsystem, additional notes can be found here. The notes usually refer to specific properties of some organisms or organism groups, genes that are missing but should be there and other details that might be useful for the interested user. 3703237b72cb9ffe4f3de4bfed444a236cc431b9 2310 2309 2008-12-03T18:20:23Z TobiasPaczian 17 /* Spreadsheet */ wikitext text/x-wiki == Subsystems == A [[Glossary#Subsystem|subsystem]] is a collection of [[Glossary#Functional role|functional roles]] that are associated to each other in a system. Such a system can for example be a metabolic pathway or a component of a cell like a secretion system. The subsystem page in the SeedViewer is divided into different parts via a [[WebComponents/Tabview|TabView]]. The TabView can consist of 3-5 tabs. The first tab shows a '''Diagram''' of the subsystem, the second tab displays a [[WebComponents/Table|table]] with the '''Functional Roles''' present in the subsystem. The '''Spreadsheet''' relating the functional roles in the subsystem to features in genomes can be found in the third tab. The fourth and fifth tab show a description and additional notes to a subsystem. They only appear if a subsystem has a description / notes. === Diagram === The subsystem diagram shows the connections between the functional roles in a subsystem. The boxes represent the functional roles via their abbreviations. The circles are connecting intermediates, that are described in the table which is part of the diagram. The functional roles in the diagram can be colored according to their presence in a genome. Click the button '''Color Diagram''' to get a combo box with all genomes in the subsystem. Select your genome of interest and press '''do coloring'''. The boxes for the functional roles defined for that genome will now be colored in green. [[Image:SubsystemDiagram.png]] === Functional Roles === This [[WebComponents/Table|table]] lists all functional roles present in the subsystem. The first column shows '''Group Aliases''' for the functional role. Functional roles can be aggregated in groups (subsets). Subset names that start with a '*' contain alternative ways to implement a function. The abbreviation ('''Abbrev.''') for a functional role must be unique for the functional roles in the subsystem. It is used in different displays like the Diagram or the Speadsheet. The third column lists the full name of the functional role. EC-Numbers are often part of the functional role (for enzymes), and are stated in parentheses after the name of the functional role. The following two columns deal with reactions a functional role is connected to. Clicking on the link opens a new window showing the KEGG reaction. Next to annotator-curated KEGG reactions, we show the KEGG reactions of the curation effort of the [[SEED_People#Hope College|Hope College]] team that collaborates with the SEED. GeneOntology (GO) links are displayed in the next column. The links point to the GO-number in GeneOntology's Amigo-Tool. The last column can contain literature (PubMed IDs) that describes the functional role in detail. If present, you will find a link to PubMed in this column. [[Image:SubsystemFRs.png]] === Spreadsheet === The subsystem spreadsheet displays the features that are assigned with the functional roles in all organisms that are part of the subsystem. The organisms are displayed in the first column. The links lead to the [[SEED_Viewer_Manual/OrganismPage|Organism Page]]. The column header includes a filter option for the organism, doing an infix search on the organism name. The '''Domain''' (Bacterial, Archaeal or Eukaryote) of the organism is shown in the second column. For each organism in the spreadsheet, a '''Variant Code''' is assigned. Usually, there is more than one way to fulfill a subsystem. Metabolic pathways can have alternatives, or parts of the pathway may be present or absent in an organism. [[Glossary/Variant Code|Variant Codes]] are assigned to the organism to express this behavior. There are two special Variant Codes: '''0''' and '''-1'''. The Variant Code '''-1''' means that the organism has no active variant in this subsystem, meaning it does not implement the subsystem. '''0''' means that the curator has not yet assigned a variant to the genome. Due to the flow of newly sequenced genomes into the SEED, this variant code may show up sometimes. The next column is used to filter active or inactive variants. If you want to see only the active ones (default), enter '''yes''' into the filter in the column header. For seeing only the not active ones, enter '''no'''. No input in this field will show all variants. All following columns in the table show the features in the organisms that are assigned with functional roles. The column headers display the abbreviations of the functional roles (see Functional Roles Table) Hovering over a column header will show a tooltip with the full name of the role. The feature entries in the cells for the functional roles are linked to the [[SEED_Viewer_Manual/Annotation|Annotation Page]] for that feature. There can be multiple features in a cell, as some functions are implemented by more that one feature in an organism. The control table on top of the spreadsheet table lets you change the display in the table: Functional Roles that belong to a subset starting with a '*', meaning they are alternatives for a function, are collapsed in the spreadsheet by default. If you want to expand the subsets, you can do so by checking '''expanded''' in the '''Subsets''' column. The feature entries in the spreadsheet can be colored according to different metaphors using the second column ('''Coloring''') of the table. By default, the features are colored '''by cluster'''. In this case, it is computed which features are close by on the genomic sequence, meaning they cluster. Each computed cluster gets its own color. These colors only have a meaning per genome, meaning that a yellow cluster in one genome has no connection to a yellow cluster in the next genome. Another way to cluster the features are different kinds of attributes. Check the radio box for '''by attribute''' and choose an attribute in the drop down menu. Press '''update''' to change the display. [[Image:SubsystemSpreadsheet.png]] === Description === The description of a subsystem gives an overview of the functional roles and their connections in the subsystem. It can give some background information about the system, what organisms it is usually found in and other facts that are of interest. === Additional Notes === As the description already gives an overview over the subsystem, additional notes can be found here. The notes usually refer to specific properties of some organisms or organism groups, genes that are missing but should be there and other details that might be useful for the interested user. 86500f4150cfb717cd510e87bb18e30ab8b49b14 2331 2310 2008-12-03T19:21:35Z TobiasPaczian 17 /* Spreadsheet */ wikitext text/x-wiki == Subsystems == A [[Glossary#Subsystem|subsystem]] is a collection of [[Glossary#Functional role|functional roles]] that are associated to each other in a system. Such a system can for example be a metabolic pathway or a component of a cell like a secretion system. The subsystem page in the SeedViewer is divided into different parts via a [[WebComponents/Tabview|TabView]]. The TabView can consist of 3-5 tabs. The first tab shows a '''Diagram''' of the subsystem, the second tab displays a [[WebComponents/Table|table]] with the '''Functional Roles''' present in the subsystem. The '''Spreadsheet''' relating the functional roles in the subsystem to features in genomes can be found in the third tab. The fourth and fifth tab show a description and additional notes to a subsystem. They only appear if a subsystem has a description / notes. === Diagram === The subsystem diagram shows the connections between the functional roles in a subsystem. The boxes represent the functional roles via their abbreviations. The circles are connecting intermediates, that are described in the table which is part of the diagram. The functional roles in the diagram can be colored according to their presence in a genome. Click the button '''Color Diagram''' to get a combo box with all genomes in the subsystem. Select your genome of interest and press '''do coloring'''. The boxes for the functional roles defined for that genome will now be colored in green. [[Image:SubsystemDiagram.png]] === Functional Roles === This [[WebComponents/Table|table]] lists all functional roles present in the subsystem. The first column shows '''Group Aliases''' for the functional role. Functional roles can be aggregated in groups (subsets). Subset names that start with a '*' contain alternative ways to implement a function. The abbreviation ('''Abbrev.''') for a functional role must be unique for the functional roles in the subsystem. It is used in different displays like the Diagram or the Speadsheet. The third column lists the full name of the functional role. EC-Numbers are often part of the functional role (for enzymes), and are stated in parentheses after the name of the functional role. The following two columns deal with reactions a functional role is connected to. Clicking on the link opens a new window showing the KEGG reaction. Next to annotator-curated KEGG reactions, we show the KEGG reactions of the curation effort of the [[SEED_People#Hope College|Hope College]] team that collaborates with the SEED. GeneOntology (GO) links are displayed in the next column. The links point to the GO-number in GeneOntology's Amigo-Tool. The last column can contain literature (PubMed IDs) that describes the functional role in detail. If present, you will find a link to PubMed in this column. [[Image:SubsystemFRs.png]] === Spreadsheet === The subsystem spreadsheet displays the features that are assigned with the functional roles in all organisms that are part of the subsystem. The organisms are displayed in the first column. The links lead to the [[SEED_Viewer_Manual/OrganismPage|Organism Page]]. The column header includes a filter option for the organism, doing an infix search on the organism name. The '''Domain''' (Bacterial, Archaeal or Eukaryote) of the organism is shown in the second column. For each organism in the spreadsheet, a '''Variant Code''' is assigned. Usually, there is more than one way to fulfill a subsystem. Metabolic pathways can have alternatives, or parts of the pathway may be present or absent in an organism. [[Glossary/Variant Code|Variant Codes]] are assigned to the organism to express this behavior. There are two special Variant Codes: '''0''' and '''-1'''. The Variant Code '''-1''' means that the organism has no active variant of this subsystem, it is not implement this organism. '''0''' means that the curator has not yet assigned a variant to the genome. Due to the flow of newly sequenced genomes into the SEED, this variant code may show up sometimes. The next column is used to filter active or inactive variants. If you want to see only the active ones (default), enter '''yes''' into the filter in the column header. For seeing only the not active ones, enter '''no'''. No input in this field will show all variants. All following columns in the table show the features in the organisms that are assigned with functional roles. The column headers display the abbreviations of the functional roles (see Functional Roles Table) Hovering over a column header will show a tooltip with the full name of the role. The feature entries in the cells for the functional roles are linked to the [[SEED_Viewer_Manual/Annotation|Annotation Page]] for that feature. There can be multiple features in a cell, as some functions are implemented by more that one feature in an organism. The control table on top of the spreadsheet table lets you change the display in the table: Functional Roles that belong to a subset starting with a '*', meaning they are alternatives for a function, are collapsed in the spreadsheet by default. If you want to expand the subsets, you can do so by checking '''expanded''' in the '''Subsets''' column. The feature entries in the spreadsheet can be colored according to different metaphors using the second column ('''Coloring''') of the table. By default, the features are colored '''by cluster'''. In this case, it is computed which features are close by on the genomic sequence, meaning they cluster. Each computed cluster gets its own color. These colors only have a meaning per genome, meaning that a yellow cluster in one genome has no connection to a yellow cluster in the next genome. Another way to cluster the features are different kinds of attributes. Check the radio box for '''by attribute''' and choose an attribute in the drop down menu. Press '''update''' to change the display. [[Image:SubsystemSpreadsheet.png]] === Description === The description of a subsystem gives an overview of the functional roles and their connections in the subsystem. It can give some background information about the system, what organisms it is usually found in and other facts that are of interest. === Additional Notes === As the description already gives an overview over the subsystem, additional notes can be found here. The notes usually refer to specific properties of some organisms or organism groups, genes that are missing but should be there and other details that might be useful for the interested user. e8cc0af7b825682403ad2dd10712bf2288edb9d4 2332 2331 2008-12-03T19:22:44Z TobiasPaczian 17 /* Spreadsheet */ wikitext text/x-wiki == Subsystems == A [[Glossary#Subsystem|subsystem]] is a collection of [[Glossary#Functional role|functional roles]] that are associated to each other in a system. Such a system can for example be a metabolic pathway or a component of a cell like a secretion system. The subsystem page in the SeedViewer is divided into different parts via a [[WebComponents/Tabview|TabView]]. The TabView can consist of 3-5 tabs. The first tab shows a '''Diagram''' of the subsystem, the second tab displays a [[WebComponents/Table|table]] with the '''Functional Roles''' present in the subsystem. The '''Spreadsheet''' relating the functional roles in the subsystem to features in genomes can be found in the third tab. The fourth and fifth tab show a description and additional notes to a subsystem. They only appear if a subsystem has a description / notes. === Diagram === The subsystem diagram shows the connections between the functional roles in a subsystem. The boxes represent the functional roles via their abbreviations. The circles are connecting intermediates, that are described in the table which is part of the diagram. The functional roles in the diagram can be colored according to their presence in a genome. Click the button '''Color Diagram''' to get a combo box with all genomes in the subsystem. Select your genome of interest and press '''do coloring'''. The boxes for the functional roles defined for that genome will now be colored in green. [[Image:SubsystemDiagram.png]] === Functional Roles === This [[WebComponents/Table|table]] lists all functional roles present in the subsystem. The first column shows '''Group Aliases''' for the functional role. Functional roles can be aggregated in groups (subsets). Subset names that start with a '*' contain alternative ways to implement a function. The abbreviation ('''Abbrev.''') for a functional role must be unique for the functional roles in the subsystem. It is used in different displays like the Diagram or the Speadsheet. The third column lists the full name of the functional role. EC-Numbers are often part of the functional role (for enzymes), and are stated in parentheses after the name of the functional role. The following two columns deal with reactions a functional role is connected to. Clicking on the link opens a new window showing the KEGG reaction. Next to annotator-curated KEGG reactions, we show the KEGG reactions of the curation effort of the [[SEED_People#Hope College|Hope College]] team that collaborates with the SEED. GeneOntology (GO) links are displayed in the next column. The links point to the GO-number in GeneOntology's Amigo-Tool. The last column can contain literature (PubMed IDs) that describes the functional role in detail. If present, you will find a link to PubMed in this column. [[Image:SubsystemFRs.png]] === Spreadsheet === The subsystem spreadsheet displays the features that are assigned with the functional roles in all organisms that are part of the subsystem. The organisms are displayed in the first column. The links lead to the [[SEED_Viewer_Manual/OrganismPage|Organism Page]]. The column header includes a filter option for the organism, doing an infix search on the organism name. The '''Domain''' (Bacterial, Archaeal or Eukaryote) of the organism is shown in the second column. For each organism in the spreadsheet, a '''Variant Code''' is assigned. Usually, there is more than one way to fulfill a subsystem. Metabolic pathways can have alternatives, or parts of the pathway may be present or absent in an organism. [[Glossary/Variant Code|Variant Codes]] are assigned to the organism to express this behavior. There are two special Variant Codes: '''0''' and '''-1'''. The Variant Code '''-1''' means that the organism has no active variant of this subsystem, it is not implement this organism. '''0''' means that the curator has not yet assigned a variant to the genome. Due to the flow of newly sequenced genomes into the SEED, this variant code may show up sometimes. The next column is used to filter active or inactive variants. If you want to see only the active ones (default), enter '''yes''' into the filter in the column header. For seeing only the not active ones, enter '''no'''. No input in this field will show all variants. All following columns in the table show the features in the organisms that are assigned with functional roles. The column headers display the abbreviations of the functional roles (see Functional Roles Table). Hovering over a column header will show a tooltip with the full name of the role. The feature entries in the cells for the functional roles are linked to the [[SEED_Viewer_Manual/Annotation|Annotation Page]] for that feature. There can be multiple features in a cell, as some functions are implemented by more that one feature in an organism. The control table on top of the spreadsheet table lets you change the display in the table: Functional Roles that belong to a subset starting with a '*', meaning they are alternatives for a function, are collapsed in the spreadsheet by default. If you want to expand the subsets, you can do so by checking '''expanded''' in the '''Subsets''' column. The feature entries in the spreadsheet can be colored according to different metaphors using the second column ('''Coloring''') of the table. By default, the features are colored '''by cluster'''. In this case, it is computed which features are close by on the genomic sequence, meaning they cluster. Each computed cluster gets its own color. These colors only have a meaning per genome, meaning that a yellow cluster in one genome has no connection to a yellow cluster in the next genome. Another way to cluster the features are different kinds of attributes. Check the radio box for '''by attribute''' and choose an attribute in the drop down menu. Press '''update''' to change the display. [[Image:SubsystemSpreadsheet.png]] === Description === The description of a subsystem gives an overview of the functional roles and their connections in the subsystem. It can give some background information about the system, what organisms it is usually found in and other facts that are of interest. === Additional Notes === As the description already gives an overview over the subsystem, additional notes can be found here. The notes usually refer to specific properties of some organisms or organism groups, genes that are missing but should be there and other details that might be useful for the interested user. 836cde806fd8e552338fce4604d6a9b0ec18ce02 0 1579 2314 2008-12-03T18:32:36Z DanielaBartels 10 wikitext text/x-wiki == FIGfam Viewer == 5195fc5fec46261eafe008805808751f25d1af60 0 1580 2316 2008-12-03T18:34:24Z DanielaBartels 10 wikitext text/x-wiki == FIGfams Page == [[Image:FIGfamsSearch1.png]] [[Image:FIGfamsSearch2.png]] [[Image:FIGfamsResult.png]] 28091a77d6b8263d48df61065ca4ec39ad62629a 2320 2316 2008-12-03T18:37:46Z DanielaBartels 10 /* FIGfams Page */ wikitext text/x-wiki == FIGfams Page == [[Image:FIGfamsSearch1.png]] [[Image:FIGfamsSearch3.png]] [[Image:FIGfamsResult.png]] 5e69e89537b4319ac776a9d812a4ab72d61b4357 2323 2320 2008-12-03T18:41:18Z DanielaBartels 10 /* FIGfams Page */ wikitext text/x-wiki == FIGfams Page == [[Image:FIGfamsSearch1.png]] [[Image:FIGfamsSearch3.png]] [[Image:FIGfamsResult1.png]] 9c285de4ea6f4c82907ab920c6f2e7cc12bfaf51 2325 2323 2008-12-03T18:44:43Z DanielaBartels 10 /* FIGfams Page */ wikitext text/x-wiki == FIGfams Page == [[Image:FIGfamsSearch1.png]] [[Image:FIGfamsResult1.png]] [[Image:FIGfamsSearch3.png]] [[Image:FIGfamsResult2.png]] 6db3b3d3369b460efb9bbcd6aeacf9a67482ffe9 2327 2325 2008-12-03T19:00:30Z DanielaBartels 10 /* FIGfams Page */ wikitext text/x-wiki == FIGfams Page == This page explains a lot about FIGfams in the text. You can also find a link to the version history and some statistics using the link '''history and statistics'''. On the right side of the page you can find two ways of accessing the FIGfams. The first text box under '''Enter FIGfam, Keyword or a sequence FIG id''' lets you enter a search text. Click return to get the result. [[Image:FIGfamsSearch1.png]] [[Image:FIGfamsResult1.png]] [[Image:FIGfamsSearch3.png]] [[Image:FIGfamsResult2.png]] 12428ba94c725b8a0060e68558409dae534f3ed1 2328 2327 2008-12-03T19:05:12Z DanielaBartels 10 /* FIGfams Page */ wikitext text/x-wiki == FIGfams Page == This page explains a lot about FIGfams in the text. You can also find a link to the version history and some statistics using the link '''history and statistics'''. On the right side of the page you can find two ways of accessing the FIGfams. The first text box under '''Enter FIGfam, Keyword or a sequence FIG id''' lets you enter a search text. Click return to get the result. [[Image:FIGfamsSearch1.png]] The result of the search is a three-column table with hits. The '''FIGfam ID''' links to the [[SEED_Viewer_Manual/FIGfamViewer|FIGfam Viewer Page]] for the FIGfam hit. - Function - Sequence Quantity [[Image:FIGfamsResult1.png]] [[Image:FIGfamsSearch3.png]] [[Image:FIGfamsResult2.png]] 2e0ed5c5fbcd73f598e2a73c2c0f4d0a702572fd 2329 2328 2008-12-03T19:06:21Z DanielaBartels 10 /* FIGfams Page */ wikitext text/x-wiki == FIGfams Page == This page explains a lot about FIGfams in the text. You can also find a link to the version history and some statistics using the link '''history and statistics'''. On the right side of the page you can find two ways of accessing the FIGfams. The first text box under '''Enter FIGfam, Keyword or a sequence FIG id''' lets you enter a search text. Click return to get the result. [[Image:FIGfamsSearch1.png]] The result of the search is a three-column table with hits. The '''FIGfam ID''' links to the [[SEED_Viewer_Manual/FIGfamViewer|FIGfam Viewer Page]] for the FIGfam hit. The '''Function''' is the functional role assigned to the FIGfam. The number of sequences that belong to the FIGfam is displayed in the column '''Sequence Quantity'''. [[Image:FIGfamsResult1.png]] [[Image:FIGfamsSearch3.png]] [[Image:FIGfamsResult2.png]] b31f5beccd0fca352a3ba63801f544624a899995 2330 2329 2008-12-03T19:17:22Z DanielaBartels 10 /* FIGfams Page */ wikitext text/x-wiki == FIGfams Page == This page explains a lot about FIGfams in the text. You can also find a link to the version history and some statistics using the link '''history and statistics'''. On the right side of the page you can find two ways of accessing the FIGfams. The first text box under '''Enter FIGfam, Keyword or a sequence FIG id''' lets you enter a search text. Click return to get the result. [[Image:FIGfamsSearch1.png]] The result of the search is a three-column table with hits. The '''FIGfam ID''' links to the [[SEED_Viewer_Manual/FIGfamViewer|FIGfam Viewer Page]] for the FIGfam hit. The '''Function''' is the functional role assigned to the FIGfam. The number of sequences that belong to the FIGfam is displayed in the column '''Sequence Quantity'''. [[Image:FIGfamsResult1.png]] The second search you can do is paste a fasta sequence into the second text field under '''Or scan a fasta sequence against the FIGfams'''. Press the button '''search''' to get the results. [[Image:FIGfamsSearch3.png]] In this case, you will find the best hit of your sequence against the FIGfams. The '''Hit family''' links to the [[SEED_Viewer_Manual/FIGfamViewer|FIGfam Viewer Page]] of the FIGfam. [[Image:FIGfamsResult2.png]] 2b9f2b44efbb3314f346188c73484aed3c9a1c9c 6 1581 2317 2008-12-03T18:36:06Z DanielaBartels 10 wikitext text/x-wiki da39a3ee5e6b4b0d3255bfef95601890afd80709 6 1584 2321 2008-12-03T18:37:59Z DanielaBartels 10 wikitext text/x-wiki da39a3ee5e6b4b0d3255bfef95601890afd80709 6 1586 2324 2008-12-03T18:41:39Z DanielaBartels 10 wikitext text/x-wiki da39a3ee5e6b4b0d3255bfef95601890afd80709 6 1587 2326 2008-12-03T18:45:05Z DanielaBartels 10 wikitext text/x-wiki da39a3ee5e6b4b0d3255bfef95601890afd80709 0 1517 2333 2332 2008-12-03T19:23:45Z TobiasPaczian 17 /* Spreadsheet */ wikitext text/x-wiki == Subsystems == A [[Glossary#Subsystem|subsystem]] is a collection of [[Glossary#Functional role|functional roles]] that are associated to each other in a system. Such a system can for example be a metabolic pathway or a component of a cell like a secretion system. The subsystem page in the SeedViewer is divided into different parts via a [[WebComponents/Tabview|TabView]]. The TabView can consist of 3-5 tabs. The first tab shows a '''Diagram''' of the subsystem, the second tab displays a [[WebComponents/Table|table]] with the '''Functional Roles''' present in the subsystem. The '''Spreadsheet''' relating the functional roles in the subsystem to features in genomes can be found in the third tab. The fourth and fifth tab show a description and additional notes to a subsystem. They only appear if a subsystem has a description / notes. === Diagram === The subsystem diagram shows the connections between the functional roles in a subsystem. The boxes represent the functional roles via their abbreviations. The circles are connecting intermediates, that are described in the table which is part of the diagram. The functional roles in the diagram can be colored according to their presence in a genome. Click the button '''Color Diagram''' to get a combo box with all genomes in the subsystem. Select your genome of interest and press '''do coloring'''. The boxes for the functional roles defined for that genome will now be colored in green. [[Image:SubsystemDiagram.png]] === Functional Roles === This [[WebComponents/Table|table]] lists all functional roles present in the subsystem. The first column shows '''Group Aliases''' for the functional role. Functional roles can be aggregated in groups (subsets). Subset names that start with a '*' contain alternative ways to implement a function. The abbreviation ('''Abbrev.''') for a functional role must be unique for the functional roles in the subsystem. It is used in different displays like the Diagram or the Speadsheet. The third column lists the full name of the functional role. EC-Numbers are often part of the functional role (for enzymes), and are stated in parentheses after the name of the functional role. The following two columns deal with reactions a functional role is connected to. Clicking on the link opens a new window showing the KEGG reaction. Next to annotator-curated KEGG reactions, we show the KEGG reactions of the curation effort of the [[SEED_People#Hope College|Hope College]] team that collaborates with the SEED. GeneOntology (GO) links are displayed in the next column. The links point to the GO-number in GeneOntology's Amigo-Tool. The last column can contain literature (PubMed IDs) that describes the functional role in detail. If present, you will find a link to PubMed in this column. [[Image:SubsystemFRs.png]] === Spreadsheet === The subsystem spreadsheet displays the features that are assigned with the functional roles in all organisms that are part of the subsystem. The organisms are displayed in the first column. The links lead to the [[SEED_Viewer_Manual/OrganismPage|Organism Page]]. The column header includes a filter option for the organism, doing an infix search on the organism name. The '''Domain''' (Bacterial, Archaeal or Eukaryote) of the organism is shown in the second column. For each organism in the spreadsheet, a '''Variant Code''' is assigned. Usually, there is more than one way to fulfill a subsystem. Metabolic pathways can have alternatives, or parts of the pathway may be present or absent in an organism. [[Glossary/Variant Code|Variant Codes]] are assigned to the organism to express this behavior. There are two special Variant Codes: '''0''' and '''-1'''. The Variant Code '''-1''' means that the organism has no active variant of this subsystem, it is not implement this organism. '''0''' means that the curator has not yet assigned a variant to the genome. Due to the flow of newly sequenced genomes into the SEED, this variant code may show up sometimes. The next column is used to filter active or inactive variants. If you want to see only the active ones (default), enter '''yes''' into the filter in the column header. For seeing only the not active ones, enter '''no'''. No input in this field will show all variants. All following columns in the table show the features in the organisms that are assigned with functional roles. The column headers display the abbreviations of the functional roles (see Functional Roles Table). Hovering over a column header will show a tooltip with the full name of the role. The feature entries in the cells for the functional roles are linked to the [[SEED_Viewer_Manual/Annotation|Annotation Page]] for that feature. There can be multiple features in a cell, as some functions are implemented by more that one feature in an organism. The control table above the spreadsheet table lets you change the display in the table: Functional Roles that belong to a subset starting with a '*', meaning they are alternatives for a function, are collapsed in the spreadsheet by default. If you want to expand the subsets, you can do so by checking '''expanded''' in the '''Subsets''' column. The feature entries in the spreadsheet can be colored according to different metaphors using the second column ('''Coloring''') of the table. By default, the features are colored '''by cluster'''. In this case, it is computed which features are close by on the genomic sequence, meaning they cluster. Each computed cluster gets its own color. These colors only have a meaning per genome, meaning that a yellow cluster in one genome has no connection to a yellow cluster in the next genome. Another way to cluster the features are different kinds of attributes. Check the radio box for '''by attribute''' and choose an attribute in the drop down menu. Press '''update''' to change the display. [[Image:SubsystemSpreadsheet.png]] === Description === The description of a subsystem gives an overview of the functional roles and their connections in the subsystem. It can give some background information about the system, what organisms it is usually found in and other facts that are of interest. === Additional Notes === As the description already gives an overview over the subsystem, additional notes can be found here. The notes usually refer to specific properties of some organisms or organism groups, genes that are missing but should be there and other details that might be useful for the interested user. 3ccaf6ad0c15576387c5bff0d760b49f436e1881 2359 2333 2008-12-04T13:40:44Z DanielaBartels 10 /* Subsystems */ wikitext text/x-wiki == Subsystems == A [[Glossary#Subsystem|subsystem]] is a collection of [[Glossary#Functional role|functional roles]] that are associated to each other in a system. Such a system can for example be a metabolic pathway or a component of a cell like a secretion system. The subsystem page in the SeedViewer is divided into different parts via a [[WebComponents/Tabview|TabView]]. The TabView can consist of 3-5 tabs. The first tab shows a '''Diagram''' of the subsystem, the second tab displays a [[WebComponents/Table|table]] with the '''Functional Roles''' present in the subsystem. The '''Spreadsheet''' relating the functional roles in the subsystem to features in genomes can be found in the third tab. The fourth and fifth tab show a description and additional notes to a subsystem. They only appear if a subsystem has a description / notes. The last tab displays the [[Glossary#Scenarios|Scenarios]] for the subsystem. === Diagram === The subsystem diagram shows the connections between the functional roles in a subsystem. The boxes represent the functional roles via their abbreviations. The circles are connecting intermediates, that are described in the table which is part of the diagram. The functional roles in the diagram can be colored according to their presence in a genome. Click the button '''Color Diagram''' to get a combo box with all genomes in the subsystem. Select your genome of interest and press '''do coloring'''. The boxes for the functional roles defined for that genome will now be colored in green. [[Image:SubsystemDiagram.png]] === Functional Roles === This [[WebComponents/Table|table]] lists all functional roles present in the subsystem. The first column shows '''Group Aliases''' for the functional role. Functional roles can be aggregated in groups (subsets). Subset names that start with a '*' contain alternative ways to implement a function. The abbreviation ('''Abbrev.''') for a functional role must be unique for the functional roles in the subsystem. It is used in different displays like the Diagram or the Speadsheet. The third column lists the full name of the functional role. EC-Numbers are often part of the functional role (for enzymes), and are stated in parentheses after the name of the functional role. The following two columns deal with reactions a functional role is connected to. Clicking on the link opens a new window showing the KEGG reaction. Next to annotator-curated KEGG reactions, we show the KEGG reactions of the curation effort of the [[SEED_People#Hope College|Hope College]] team that collaborates with the SEED. GeneOntology (GO) links are displayed in the next column. The links point to the GO-number in GeneOntology's Amigo-Tool. The last column can contain literature (PubMed IDs) that describes the functional role in detail. If present, you will find a link to PubMed in this column. [[Image:SubsystemFRs.png]] === Spreadsheet === The subsystem spreadsheet displays the features that are assigned with the functional roles in all organisms that are part of the subsystem. The organisms are displayed in the first column. The links lead to the [[SEED_Viewer_Manual/OrganismPage|Organism Page]]. The column header includes a filter option for the organism, doing an infix search on the organism name. The '''Domain''' (Bacterial, Archaeal or Eukaryote) of the organism is shown in the second column. For each organism in the spreadsheet, a '''Variant Code''' is assigned. Usually, there is more than one way to fulfill a subsystem. Metabolic pathways can have alternatives, or parts of the pathway may be present or absent in an organism. [[Glossary/Variant Code|Variant Codes]] are assigned to the organism to express this behavior. There are two special Variant Codes: '''0''' and '''-1'''. The Variant Code '''-1''' means that the organism has no active variant of this subsystem, it is not implement this organism. '''0''' means that the curator has not yet assigned a variant to the genome. Due to the flow of newly sequenced genomes into the SEED, this variant code may show up sometimes. The next column is used to filter active or inactive variants. If you want to see only the active ones (default), enter '''yes''' into the filter in the column header. For seeing only the not active ones, enter '''no'''. No input in this field will show all variants. All following columns in the table show the features in the organisms that are assigned with functional roles. The column headers display the abbreviations of the functional roles (see Functional Roles Table). Hovering over a column header will show a tooltip with the full name of the role. The feature entries in the cells for the functional roles are linked to the [[SEED_Viewer_Manual/Annotation|Annotation Page]] for that feature. There can be multiple features in a cell, as some functions are implemented by more that one feature in an organism. The control table above the spreadsheet table lets you change the display in the table: Functional Roles that belong to a subset starting with a '*', meaning they are alternatives for a function, are collapsed in the spreadsheet by default. If you want to expand the subsets, you can do so by checking '''expanded''' in the '''Subsets''' column. The feature entries in the spreadsheet can be colored according to different metaphors using the second column ('''Coloring''') of the table. By default, the features are colored '''by cluster'''. In this case, it is computed which features are close by on the genomic sequence, meaning they cluster. Each computed cluster gets its own color. These colors only have a meaning per genome, meaning that a yellow cluster in one genome has no connection to a yellow cluster in the next genome. Another way to cluster the features are different kinds of attributes. Check the radio box for '''by attribute''' and choose an attribute in the drop down menu. Press '''update''' to change the display. [[Image:SubsystemSpreadsheet.png]] === Description === The description of a subsystem gives an overview of the functional roles and their connections in the subsystem. It can give some background information about the system, what organisms it is usually found in and other facts that are of interest. === Additional Notes === As the description already gives an overview over the subsystem, additional notes can be found here. The notes usually refer to specific properties of some organisms or organism groups, genes that are missing but should be there and other details that might be useful for the interested user. === Scenarios === The table shows all scenarios that occur in the subsystem. You can see the scenario name, the '''Input Compounds''', the '''Output Compounds''' and a checkbox to decide if you want to see the scenario painted on the [http://www.genome.jp/kegg/ KEGG] map below. [[Image:SubsystemScenTabs.png]] [[Image:SubsystemScenarios.png]] 8d4a803e97dd5a795e19589f96bfbb6438967d5c 2360 2359 2008-12-04T13:48:48Z DanielaBartels 10 /* Scenarios */ wikitext text/x-wiki == Subsystems == A [[Glossary#Subsystem|subsystem]] is a collection of [[Glossary#Functional role|functional roles]] that are associated to each other in a system. Such a system can for example be a metabolic pathway or a component of a cell like a secretion system. The subsystem page in the SeedViewer is divided into different parts via a [[WebComponents/Tabview|TabView]]. The TabView can consist of 3-5 tabs. The first tab shows a '''Diagram''' of the subsystem, the second tab displays a [[WebComponents/Table|table]] with the '''Functional Roles''' present in the subsystem. The '''Spreadsheet''' relating the functional roles in the subsystem to features in genomes can be found in the third tab. The fourth and fifth tab show a description and additional notes to a subsystem. They only appear if a subsystem has a description / notes. The last tab displays the [[Glossary#Scenarios|Scenarios]] for the subsystem. === Diagram === The subsystem diagram shows the connections between the functional roles in a subsystem. The boxes represent the functional roles via their abbreviations. The circles are connecting intermediates, that are described in the table which is part of the diagram. The functional roles in the diagram can be colored according to their presence in a genome. Click the button '''Color Diagram''' to get a combo box with all genomes in the subsystem. Select your genome of interest and press '''do coloring'''. The boxes for the functional roles defined for that genome will now be colored in green. [[Image:SubsystemDiagram.png]] === Functional Roles === This [[WebComponents/Table|table]] lists all functional roles present in the subsystem. The first column shows '''Group Aliases''' for the functional role. Functional roles can be aggregated in groups (subsets). Subset names that start with a '*' contain alternative ways to implement a function. The abbreviation ('''Abbrev.''') for a functional role must be unique for the functional roles in the subsystem. It is used in different displays like the Diagram or the Speadsheet. The third column lists the full name of the functional role. EC-Numbers are often part of the functional role (for enzymes), and are stated in parentheses after the name of the functional role. The following two columns deal with reactions a functional role is connected to. Clicking on the link opens a new window showing the KEGG reaction. Next to annotator-curated KEGG reactions, we show the KEGG reactions of the curation effort of the [[SEED_People#Hope College|Hope College]] team that collaborates with the SEED. GeneOntology (GO) links are displayed in the next column. The links point to the GO-number in GeneOntology's Amigo-Tool. The last column can contain literature (PubMed IDs) that describes the functional role in detail. If present, you will find a link to PubMed in this column. [[Image:SubsystemFRs.png]] === Spreadsheet === The subsystem spreadsheet displays the features that are assigned with the functional roles in all organisms that are part of the subsystem. The organisms are displayed in the first column. The links lead to the [[SEED_Viewer_Manual/OrganismPage|Organism Page]]. The column header includes a filter option for the organism, doing an infix search on the organism name. The '''Domain''' (Bacterial, Archaeal or Eukaryote) of the organism is shown in the second column. For each organism in the spreadsheet, a '''Variant Code''' is assigned. Usually, there is more than one way to fulfill a subsystem. Metabolic pathways can have alternatives, or parts of the pathway may be present or absent in an organism. [[Glossary/Variant Code|Variant Codes]] are assigned to the organism to express this behavior. There are two special Variant Codes: '''0''' and '''-1'''. The Variant Code '''-1''' means that the organism has no active variant of this subsystem, it is not implement this organism. '''0''' means that the curator has not yet assigned a variant to the genome. Due to the flow of newly sequenced genomes into the SEED, this variant code may show up sometimes. The next column is used to filter active or inactive variants. If you want to see only the active ones (default), enter '''yes''' into the filter in the column header. For seeing only the not active ones, enter '''no'''. No input in this field will show all variants. All following columns in the table show the features in the organisms that are assigned with functional roles. The column headers display the abbreviations of the functional roles (see Functional Roles Table). Hovering over a column header will show a tooltip with the full name of the role. The feature entries in the cells for the functional roles are linked to the [[SEED_Viewer_Manual/Annotation|Annotation Page]] for that feature. There can be multiple features in a cell, as some functions are implemented by more that one feature in an organism. The control table above the spreadsheet table lets you change the display in the table: Functional Roles that belong to a subset starting with a '*', meaning they are alternatives for a function, are collapsed in the spreadsheet by default. If you want to expand the subsets, you can do so by checking '''expanded''' in the '''Subsets''' column. The feature entries in the spreadsheet can be colored according to different metaphors using the second column ('''Coloring''') of the table. By default, the features are colored '''by cluster'''. In this case, it is computed which features are close by on the genomic sequence, meaning they cluster. Each computed cluster gets its own color. These colors only have a meaning per genome, meaning that a yellow cluster in one genome has no connection to a yellow cluster in the next genome. Another way to cluster the features are different kinds of attributes. Check the radio box for '''by attribute''' and choose an attribute in the drop down menu. Press '''update''' to change the display. [[Image:SubsystemSpreadsheet.png]] === Description === The description of a subsystem gives an overview of the functional roles and their connections in the subsystem. It can give some background information about the system, what organisms it is usually found in and other facts that are of interest. === Additional Notes === As the description already gives an overview over the subsystem, additional notes can be found here. The notes usually refer to specific properties of some organisms or organism groups, genes that are missing but should be there and other details that might be useful for the interested user. === Scenarios === The table shows all scenarios that occur in the subsystem. You can see the scenario name, the '''Input Compounds''', the '''Output Compounds''' and a checkbox to decide if you want to see the scenario painted on the [http://www.genome.jp/kegg/ KEGG] map below. If you change the selection of scenarios to paint on the map, click the button '''Paint Map(s)''' to reload the map. You can also select an organism to highlight on the map. Therefore, click the '''Select Organism''' button to get an [[SEED_Viewer_Manual/OrganismSelect]]. After choosing an organism, click the button '''Highlight Reactions for Organism''' to mark the enzymes present in the organism with black boxes. [[Image:SubsystemScenTabs.png]] The [http://www.genome.jp/kegg/ KEGG] map is the first tab of a [[WebComponents/Tabview|TabView]]. The header of the tab includes a link to the map at [http://www.genome.jp/kegg/ KEGG]. Each enzyme in the map is painted with all colors of the scenarios it is part of. A color legend is presented on the right side of the map. The second tab of the [[WebComponents/Tabview|TabView]] shows all reactions that are not shown on the map, but are part of the subsystem. [[Image:SubsystemScenarios.png]] 98a78c79912f41faa52a619115bcaa0eaef02d01 0 1579 2334 2314 2008-12-03T19:24:54Z DanielaBartels 10 /* FIGfam Viewer */ wikitext text/x-wiki == FIGfam Viewer == [[Image:FIGfamViewerTable.png]] f426003794dceed55df3a8d8e44b4acdd8ccfab9 2337 2334 2008-12-03T19:30:52Z DanielaBartels 10 /* FIGfam Viewer */ wikitext text/x-wiki == FIGfam Viewer == The table on the top of the page displays the '''FIGfam ID''' and the '''Functional Role''' associated to the FIGfam. Subsystems that are associated with members of the FIGfam are displayed in the third row ('''Subsystems''') of the table. They are linked to the [[SEED_Viewer_Manual/Subsystems|Subsystems Page]] of the subsystem. [[Image:FIGfamViewerTable.png]] 05e7f837b87398ea599eaca17bdbbd67f02c52d0 2338 2337 2008-12-03T19:33:40Z DanielaBartels 10 /* FIGfam Viewer */ wikitext text/x-wiki == FIGfam Viewer == The table on the top of the page displays the '''FIGfam ID''' and the '''Functional Role''' associated to the FIGfam. Subsystems that are associated with members of the FIGfam are displayed in the third row ('''Subsystems''') of the table. They are linked to the [[SEED_Viewer_Manual/Subsystems|Subsystems Page]] of the subsystem. The '''FIGfam Size''' is the number of members of the FIGfam. The '''Average Sequence Length''' is the medium of aminoacids sequence length of the members of the FIGfam. Behind this there is a short statistics telling you the member with the '''Maximum length''', '''Minimum length''' and the '''Standard Deviation'''. [[Image:FIGfamViewerTable.png]] 8de7d47b051d2457a54667cb8883d342b1ddcef5 2339 2338 2008-12-03T19:41:26Z DanielaBartels 10 /* FIGfam Viewer */ wikitext text/x-wiki == FIGfam Viewer == The table on the top of the page displays the '''FIGfam ID''' and the '''Functional Role''' associated to the FIGfam. Subsystems that are associated with members of the FIGfam are displayed in the third row ('''Subsystems''') of the table. They are linked to the [[SEED_Viewer_Manual/Subsystems|Subsystems Page]] of the subsystem. The '''FIGfam Size''' is the number of members of the FIGfam. The '''Average Sequence Length''' is the medium of aminoacids sequence length of the members of the FIGfam. Behind this there is a short statistics telling you the member with the '''Maximum length''', '''Minimum length''' and the '''Standard Deviation'''. The '''Member list''' is a [[WebComponents/Table|table]] showing the '''ID''' of the member, the '''Organism''' it belongs to, '''Associated Subsystem''' (there can be more than one) and the function of the member. [[Image:FIGfamViewerTable.png]] 2f91d1c58bd58c0ae0ee568798796e1414e3179a 2340 2339 2008-12-03T19:47:10Z DanielaBartels 10 /* FIGfam Viewer */ wikitext text/x-wiki == FIGfam Viewer == The table on the top of the page displays the '''FIGfam ID''' and the '''Functional Role''' associated to the FIGfam. Subsystems that are associated with members of the FIGfam are displayed in the third row ('''Subsystems''') of the table. They are linked to the [[SEED_Viewer_Manual/Subsystems|Subsystems Page]] of the subsystem. The '''FIGfam Size''' is the number of members of the FIGfam. The '''Average Sequence Length''' is the medium of aminoacids sequence length of the members of the FIGfam. Behind this there is a short statistics telling you the member with the '''Maximum length''', '''Minimum length''' and the '''Standard Deviation'''. The '''Member list''' is a [[WebComponents/Table|table]] showing the '''ID''' of the member (the link leads to the [[SEED_Viewer_Manual/Annotation|Annotation Page]]), the '''Organism''' it belongs to, '''Associated Subsystem''' (there can be more than one) and the function of the member. You can export the list in ''tab-separated format'' using the '''export table''' button. For downloading a fasta file of the protein sequences of the members, press the '''Fasta''' button on the left. [[Image:FIGfamViewerTable.png]] 171f42e01f801938607d2260ff07150acecc8249 2341 2340 2008-12-03T19:50:40Z DanielaBartels 10 /* FIGfam Viewer */ wikitext text/x-wiki == FIGfam Viewer == The table on the top of the page displays the '''FIGfam ID''' and the '''Functional Role''' associated to the FIGfam. Subsystems that are associated with members of the FIGfam are displayed in the third row ('''Subsystems''') of the table. They are linked to the [[SEED_Viewer_Manual/Subsystems|Subsystems Page]] of the subsystem. The '''FIGfam Size''' is the number of members of the FIGfam. The '''Average Sequence Length''' is the medium of aminoacids sequence length of the members of the FIGfam. Behind this there is a short statistics telling you the member with the '''Maximum length''', '''Minimum length''' and the '''Standard Deviation'''. The '''Member list''' is a [[WebComponents/Table|table]] showing the '''ID''' of the member (the link leads to the [[SEED_Viewer_Manual/Annotation|Annotation Page]]), the '''Organism''' it belongs to, '''Associated Subsystem''' (there can be more than one) and the function of the member. You can export the list in ''tab-separated format'' using the '''export table''' button. For downloading a fasta file of the protein sequences of the members, press the '''Fasta''' button on the left. [[Image:FIGfamViewerTable.png]] [[Image::FIGfamViewerTree.png]] d18d40a8c0136a9d7bd9836b2858cbab20d9bda0 2343 2341 2008-12-03T19:51:15Z DanielaBartels 10 /* FIGfam Viewer */ wikitext text/x-wiki == FIGfam Viewer == The table on the top of the page displays the '''FIGfam ID''' and the '''Functional Role''' associated to the FIGfam. Subsystems that are associated with members of the FIGfam are displayed in the third row ('''Subsystems''') of the table. They are linked to the [[SEED_Viewer_Manual/Subsystems|Subsystems Page]] of the subsystem. The '''FIGfam Size''' is the number of members of the FIGfam. The '''Average Sequence Length''' is the medium of aminoacids sequence length of the members of the FIGfam. Behind this there is a short statistics telling you the member with the '''Maximum length''', '''Minimum length''' and the '''Standard Deviation'''. The '''Member list''' is a [[WebComponents/Table|table]] showing the '''ID''' of the member (the link leads to the [[SEED_Viewer_Manual/Annotation|Annotation Page]]), the '''Organism''' it belongs to, '''Associated Subsystem''' (there can be more than one) and the function of the member. You can export the list in ''tab-separated format'' using the '''export table''' button. For downloading a fasta file of the protein sequences of the members, press the '''Fasta''' button on the left. [[Image:FIGfamViewerTable.png]] [[Image:FIGfamViewerTree.png]] 04ef126bf049900ae5b287efb4285fe7864bfeb8 2344 2343 2008-12-03T19:59:59Z DanielaBartels 10 /* FIGfam Viewer */ wikitext text/x-wiki == FIGfam Viewer == The table on the top of the page displays the '''FIGfam ID''' and the '''Functional Role''' associated to the FIGfam. Subsystems that are associated with members of the FIGfam are displayed in the third row ('''Subsystems''') of the table. They are linked to the [[SEED_Viewer_Manual/Subsystems|Subsystems Page]] of the subsystem. The '''FIGfam Size''' is the number of members of the FIGfam. The '''Average Sequence Length''' is the medium of aminoacids sequence length of the members of the FIGfam. Behind this there is a short statistics telling you the member with the '''Maximum length''', '''Minimum length''' and the '''Standard Deviation'''. The '''Member list''' is a [[WebComponents/Table|table]] showing the '''ID''' of the member (the link leads to the [[SEED_Viewer_Manual/Annotation|Annotation Page]]), the '''Organism''' it belongs to, '''Associated Subsystem''' (there can be more than one) and the function of the member. You can export the list in ''tab-separated format'' using the '''export table''' button. For downloading a fasta file of the protein sequences of the members, press the '''Fasta''' button on the left. [[Image:FIGfamViewerTable.png]] The bottom part of the page shows a '''Compare Regions View''' of the members of the FIGfam. The right graphics is a '''Compare Regions''' just like the one on the [[SEED_Viewer_Manual/Annotation|Annotation Page]]. Click [[SEED_Viewer_Manual/Annotation#Compare Regions|here]] to get a description. [[Image:FIGfamViewerTree.png]] 4f416ef0fcdbf62778be3a5f81e2423c8004e00b 2346 2344 2008-12-03T20:07:13Z DanielaBartels 10 /* FIGfam Viewer */ wikitext text/x-wiki == FIGfam Viewer == The table on the top of the page displays the '''FIGfam ID''' and the '''Functional Role''' associated to the FIGfam. Subsystems that are associated with members of the FIGfam are displayed in the third row ('''Subsystems''') of the table. They are linked to the [[SEED_Viewer_Manual/Subsystems|Subsystems Page]] of the subsystem. The '''FIGfam Size''' is the number of members of the FIGfam. The '''Average Sequence Length''' is the medium of aminoacids sequence length of the members of the FIGfam. Behind this there is a short statistics telling you the member with the '''Maximum length''', '''Minimum length''' and the '''Standard Deviation'''. The '''Member list''' is a [[WebComponents/Table|table]] showing the '''ID''' of the member (the link leads to the [[SEED_Viewer_Manual/Annotation|Annotation Page]]), the '''Organism''' it belongs to, '''Associated Subsystem''' (there can be more than one) and the function of the member. You can export the list in ''tab-separated format'' using the '''export table''' button. For downloading a fasta file of the protein sequences of the members, press the '''Fasta''' button on the left. [[Image:FIGfamViewerTable.png]] The bottom part of the page shows a '''Compare Regions View''' of the members of the FIGfam. The right graphics is a '''Compare Regions''' just like the one on the [[SEED_Viewer_Manual/Annotation|Annotation Page]]. Click [[SEED_Viewer_Manual/Annotation#Compare Regions|here]] to get a learn more. The left part is used to filter the Compare Regions View. It is an phylogenetic tree showing only the phyla with members for the FIGfam. Click the '''+''' signs to expand and '''-''' signs to collapse a part. You can deselect check boxes to remove the organisms from the Compare Regions View. Press '''Refresh Context''' to update the View. If you want to find a member of the FIGfam, you can put the ID into the text field on top of the tree. Clicking the '''search in tree''' button will expand the tree up to the position of the FIGfam member. The button '''get selected fasta''' will let you download the fasta sequences of all members in the organisms you have selected in the tree. [[Image:FIGfamViewerTree.png]] ff7d3e9e97b62be8e28f35b2c871c1d8c7d75548 6 1588 2335 2008-12-03T19:25:08Z DanielaBartels 10 wikitext text/x-wiki da39a3ee5e6b4b0d3255bfef95601890afd80709 0 1544 2336 2212 2008-12-03T19:30:43Z TobiasPaczian 17 /* Functional Role Page */ wikitext text/x-wiki == Functional Role Page == This page displays a functional role in context of a subsystem. The left part of the top table shows the '''Functional Role''' and the context '''Subsystem'''. If present, an '''EC-number''' or '''GO-number''' and '''Reactions''' are listed. The EC-number links to the [http://www.genome.ad.jp/kegg/ KEGG] enzyme page for the enzyme. GO-numbers are [http://www.geneontology.org GeneOntology] classifications for a role. The link leads to the GO-Viewer [http://amigo.geneontology.org/cgi-bin/amigo/search.cgi AmiGo]. Reactions are [http://www.genome.ad.jp/kegg/ KEGG] reactions that are bound to the EC-number. The right part of the table gives an overview of the assignments of the functional role to SEED features. '''Number of Occurrences''' is the total number of features that are assigned with the role. '''Number of Organisms''' is the number of different organisms that contain at least one feature assigned with the role. Then they are devided by domains of the organisms (Archaea, Bacteria, Eukaryota or Virus). [[Image:FunctionalRole1.png]] The table below lists all features that are assigned with the functional role. The feature ID links to the [[SEED_Viewer_Manual/Annotation|Annotation page]] for the feature. The organism link in the second column of the table points to the [[SEED_Viewer_Manual/OrganismPage|Organism Page]] for that organism. The domain of the organism is depicted in the third column. You can download the table in ''comma-separated format'' using the '''export table''' button. To gain access the sequences of the listed features, press the '''show sequences''' button that opens the [[SEED_Viewer_Manual/ShowSeqs|Sequence]] page. [[Image:FunctionalRole2.png]] f0a88d71d251ddfff3f3d4e654ecb489ce429e2a 6 1589 2342 2008-12-03T19:51:03Z DanielaBartels 10 wikitext text/x-wiki da39a3ee5e6b4b0d3255bfef95601890afd80709 0 1493 2345 2010 2008-12-03T20:02:36Z TobiasPaczian 17 /* Compare Regions */ wikitext text/x-wiki == Annotation == The Annotation page shows a variaty of information about a single feature like a protein or an RNA. The page is roughly divided into three parts. The '''Annotation Overview''' presents the basic information about the feature. '''Reasons for Current Assignment''' reflect why the feature was assigned with the current functional role. The third part is a '''Compare Regions View''' showing the region of the feature in context to its own and related genomes. If you are logged in and the feature belongs to your private genome, this page will have additional options for you to annotate the feature. These are described [[SEED_Viewer_Manual/Editing_Capabilities/Annotation|here]]. === The Annotation Overview === The feature ID and the genome it belongs to are shown in the header line of this part of the page. They link to [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] and the [[SEED_Viewer_Manual/OrganismPage|Organism Page]], respectively. The '''current annotation''' depicts the functional role that is currently assigned to the feature. As annotations can be changed by users, you have the option to view an annotation history by pressing the '''show''' button in the cell '''annotation history''' some rows below. It will open a small table listing the date, the curator and the annotation that was made for each entry. As the genome name for the feature is already presented in the header of this section, we additionally show the '''taxonomy id''' for that genome in the overview. The link will lead to the Taxonomy Browser at the NCBI showing the taxonomy information for that genome. Behind the taxonomy for the genome you can find the '''contig''' the feature can be found on. The '''internal links''' you can see in the next row are leading to different pages containing other views and information for the feature. The [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] ('''genome browser''') displays the feature in the context of its genome. '''evidence''' leads to the [[SEED_Viewer_Manual/Evidence|Evidence]] page showing evidence for the annotation of the feature in form of [[Glossary/Similarities|Similarities]] and protein domains. Downloading the actual sequence for the feature is possible using the [[SEED_Viewer_Manual/ShowSeqs|Sequence Page]] ('''sequence''') link. Behind the external links you find a link to the '''ACH''' essentially identical genes. This link leads to the [[AnnotationClearingHouse|Annotation Clearing House]], a collection of proteins from many different sources. Proteins that have essentially the same sequence are grouped. For a given ID, you can see all IDs from different sources that belong to this group. At '''PubMed Links''' you can see the PubMed IDs to papers linked to the NCBI Entrez Database. The PubMed IDs shown are direct literature links attached directly to a feature, so-called '''dlits'''. '''FIGfams''' are protein families based on the subsystems technology. If you find an entry in this fields, the feature is part of the stated FIGfam. The link leads to the [[SEED_Viewer_Manual/FIGfams|FIGfam Viewer]]. '''database cross references''' link the feature to its entries (Aliases) in other databases like UniProt, GenBANK and many others. To gain more information about a feature, you can run different tools (e.g. PSI-BLAST, InterPro and many others) on your feature. Select a tool and press the button '''run tool'''. [[Image:AnnotationFeat.png]] === Reasons for Current Assignment === To gain a clue about what evidence an assignment of a functional role to your feature is based on, the text in '''Reasons for Current Assignment''' summarizes important information supporting the annotation. Additional to the information in the overview table, a list of indirect literature ('''ilits''') is decribed in the text. Those are based on direct literature to similar features that have the same functional role. [[Image:AnnotationAnnot.png]] === Compare Regions === The first line of the '''Compare Regions''' is a graphical display of the region of the feature its genome. All proteins are shown as colored arrows, where the direction depicts the strand of the feature. RNAs and other features are small boxes on the line. If two features overlap, the overlapping will be drawn on an (invisible) second line. The graph is centered on the selected feature (numbered 1), which is always colored red. Below you find the same region for orthologs in other (related) organisms, also colored in red. The colors of the other features (as well as the numbers) also represent ortholog (or sometimes also paralog) features. Whenever there are at least two ortholog or paralog features of a kind, a color (and a number) is assigned to them. '''Display Options''' are divided into two ''Regular'' and ''Advanced''. In the '''Regular''' options, you can change the ''Region Size'' and the ''Number of Regions''. Changing the '''Region Size''' enables to zoom in or out of the region. Changing the '''Number of Regions''' will add or remove genomes to your display. Click '''update graphics''' to change the display. The numbers that you put in for these values will be saved as [[SEED_Viewer_Manual/Preferences|preferences]]. [[Image:AnnotationComp.png]] If you click '''Advanced''' options, you will see the default options that are used for the Compare Regions View. The '''Pinned CDS Selection''' refers to the chosen peg and its orthologs in other genomes. The selection of genomes to show in the graphics can be made by ''Similarity'' or ''PCH pin''. The default is '''Similarity''' and means that the genomes are chosen using the similarity of the selected genes to its orthologs in other genomes. A '''PCH''' means a ''pair of close homologs''. [...] In the cell '''Genome Selection''' you can choose to ''collapse close genomes''. For many organism groups, the SEED database contains a number of strains that do not differ too strongly. They can be removed from the display using this option. The genomes in the display can be sorted by '''Phylogeny''' or '''Phylogenetic distance to input CDS'''. In the first case, the genome of the selected peg may not appear on the first line any more, but the genomes in the display are sorted by the overall phylogeny. The second (default) options will show the selected CDSs region on the first line and the other genomes in order of phylogenetic distance to the peg. The '''Evalue cutoff for selection of pinned CDSs''' depicts the minimum similarity CDSs may have to the selected CDS so that the its region is displayed. Defining if CDSs are orthologs or paralogs to a given CDS and therefore colored as such can be done using the '''Evalue cutoff for coloring CDS sets'''. We have implemented two different '''Coloring algorithms''' for the display. Default is a fast algorithm that might not always be absolutely accurate. You can choose a slower, but exact algorithm for coloring if you are unsure. [[Image:AnnotationAdv.png]] The second tab of the Compare Regions tab view lists all visible features in a table, sorted by the genome they appear in. The entries in the '''ID''' column link to the Annotation page of the feature. Additional to Start, Stop, Strand and Functional Role of the feature, you can see a column ''FC'', an ''SS'', a ''Set'' and a ''CL''. '''FC''' stands for ''[[Glossary#Functional Coupling|Functionally coupled]]'', showing the number of features that are coupled to this feature via clustering genomes or other evidence. The '''SS''' column shows the subsystems the feature is in. '''Set''' is the number that is depicted above a colored feature in the graphic. The '''cluster''' buttons in the last column leads to the [[SEED_Viewer_Manual/HomologClusters|Homolog clusters]] page for that feature. [[Image:AnnotationTabl.png]] 889afeaff52b491ec75319c3286b557a1cae2cde 2363 2345 2008-12-04T14:12:11Z DanielaBartels 10 /* The Annotation Overview */ wikitext text/x-wiki == Annotation == The Annotation page shows a variaty of information about a single feature like a protein or an RNA. The page is roughly divided into three parts. The '''Annotation Overview''' presents the basic information about the feature. '''Reasons for Current Assignment''' reflect why the feature was assigned with the current functional role. The third part is a '''Compare Regions View''' showing the region of the feature in context to its own and related genomes. If you are logged in and the feature belongs to your private genome, this page will have additional options for you to annotate the feature. These are described [[SEED_Viewer_Manual/Editing_Capabilities/Annotation|here]]. === The Annotation Overview === The feature ID and the genome it belongs to are shown in the header line of this part of the page. They link to [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] and the [[SEED_Viewer_Manual/OrganismPage|Organism Page]], respectively. The '''current annotation''' depicts the functional role that is currently assigned to the feature. As annotations can be changed by users, you have the option to view an annotation history by pressing the '''show''' button in the cell '''annotation history''' some rows below. It will open a small table listing the date, the curator and the annotation that was made for each entry. As the genome name for the feature is already presented in the header of this section, we additionally show the '''taxonomy id''' for that genome in the overview. The link will lead to the Taxonomy Browser at the NCBI showing the taxonomy information for that genome. Behind the taxonomy for the genome you can find the '''contig''' the feature can be found on. The '''internal links''' you can see in the next row are leading to different pages containing other views and information for the feature. The [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] ('''genome browser''') displays the feature in the context of its genome. '''evidence''' leads to the [[SEED_Viewer_Manual/Evidence|Evidence]] page showing evidence for the annotation of the feature in form of [[Glossary#Similarities|Similarities]] and protein domains. Downloading the actual sequence for the feature is possible using the [[SEED_Viewer_Manual/ShowSeqs|Sequence Page]] ('''sequence''') link. Behind the external links you find a link to the '''ACH''' essentially identical genes. This link leads to the [[AnnotationClearingHouse|Annotation Clearing House]], a collection of proteins from many different sources. Proteins that have essentially the same sequence are grouped. For a given ID, you can see all IDs from different sources that belong to this group. At '''PubMed Links''' you can see the PubMed IDs to papers linked to the NCBI Entrez Database. The PubMed IDs shown are direct literature links attached directly to a feature, so-called '''dlits'''. '''FIGfams''' are protein families based on the subsystems technology. If you find an entry in this fields, the feature is part of the stated FIGfam. The link leads to the [[SEED_Viewer_Manual/FIGfams|FIGfam Viewer]]. '''database cross references''' link the feature to its entries (Aliases) in other databases like UniProt, GenBANK and many others. To gain more information about a feature, you can run different tools (e.g. PSI-BLAST, InterPro and many others) on your feature. Select a tool and press the button '''run tool'''. [[Image:AnnotationFeat.png]] === Reasons for Current Assignment === To gain a clue about what evidence an assignment of a functional role to your feature is based on, the text in '''Reasons for Current Assignment''' summarizes important information supporting the annotation. Additional to the information in the overview table, a list of indirect literature ('''ilits''') is decribed in the text. Those are based on direct literature to similar features that have the same functional role. [[Image:AnnotationAnnot.png]] === Compare Regions === The first line of the '''Compare Regions''' is a graphical display of the region of the feature its genome. All proteins are shown as colored arrows, where the direction depicts the strand of the feature. RNAs and other features are small boxes on the line. If two features overlap, the overlapping will be drawn on an (invisible) second line. The graph is centered on the selected feature (numbered 1), which is always colored red. Below you find the same region for orthologs in other (related) organisms, also colored in red. The colors of the other features (as well as the numbers) also represent ortholog (or sometimes also paralog) features. Whenever there are at least two ortholog or paralog features of a kind, a color (and a number) is assigned to them. '''Display Options''' are divided into two ''Regular'' and ''Advanced''. In the '''Regular''' options, you can change the ''Region Size'' and the ''Number of Regions''. Changing the '''Region Size''' enables to zoom in or out of the region. Changing the '''Number of Regions''' will add or remove genomes to your display. Click '''update graphics''' to change the display. The numbers that you put in for these values will be saved as [[SEED_Viewer_Manual/Preferences|preferences]]. [[Image:AnnotationComp.png]] If you click '''Advanced''' options, you will see the default options that are used for the Compare Regions View. The '''Pinned CDS Selection''' refers to the chosen peg and its orthologs in other genomes. The selection of genomes to show in the graphics can be made by ''Similarity'' or ''PCH pin''. The default is '''Similarity''' and means that the genomes are chosen using the similarity of the selected genes to its orthologs in other genomes. A '''PCH''' means a ''pair of close homologs''. [...] In the cell '''Genome Selection''' you can choose to ''collapse close genomes''. For many organism groups, the SEED database contains a number of strains that do not differ too strongly. They can be removed from the display using this option. The genomes in the display can be sorted by '''Phylogeny''' or '''Phylogenetic distance to input CDS'''. In the first case, the genome of the selected peg may not appear on the first line any more, but the genomes in the display are sorted by the overall phylogeny. The second (default) options will show the selected CDSs region on the first line and the other genomes in order of phylogenetic distance to the peg. The '''Evalue cutoff for selection of pinned CDSs''' depicts the minimum similarity CDSs may have to the selected CDS so that the its region is displayed. Defining if CDSs are orthologs or paralogs to a given CDS and therefore colored as such can be done using the '''Evalue cutoff for coloring CDS sets'''. We have implemented two different '''Coloring algorithms''' for the display. Default is a fast algorithm that might not always be absolutely accurate. You can choose a slower, but exact algorithm for coloring if you are unsure. [[Image:AnnotationAdv.png]] The second tab of the Compare Regions tab view lists all visible features in a table, sorted by the genome they appear in. The entries in the '''ID''' column link to the Annotation page of the feature. Additional to Start, Stop, Strand and Functional Role of the feature, you can see a column ''FC'', an ''SS'', a ''Set'' and a ''CL''. '''FC''' stands for ''[[Glossary#Functional Coupling|Functionally coupled]]'', showing the number of features that are coupled to this feature via clustering genomes or other evidence. The '''SS''' column shows the subsystems the feature is in. '''Set''' is the number that is depicted above a colored feature in the graphic. The '''cluster''' buttons in the last column leads to the [[SEED_Viewer_Manual/HomologClusters|Homolog clusters]] page for that feature. [[Image:AnnotationTabl.png]] a5ccdb1a1bb496c6cb1e288d35f100b4b32141fe 2364 2363 2008-12-04T14:14:04Z DanielaBartels 10 /* The Annotation Overview */ wikitext text/x-wiki == Annotation == The Annotation page shows a variaty of information about a single feature like a protein or an RNA. The page is roughly divided into three parts. The '''Annotation Overview''' presents the basic information about the feature. '''Reasons for Current Assignment''' reflect why the feature was assigned with the current functional role. The third part is a '''Compare Regions View''' showing the region of the feature in context to its own and related genomes. If you are logged in and the feature belongs to your private genome, this page will have additional options for you to annotate the feature. These are described [[SEED_Viewer_Manual/Editing_Capabilities/Annotation|here]]. === The Annotation Overview === The feature ID and the genome it belongs to are shown in the header line of this part of the page. They link to [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] and the [[SEED_Viewer_Manual/OrganismPage|Organism Page]], respectively. The '''current annotation''' depicts the functional role that is currently assigned to the feature. As annotations can be changed by users, you have the option to view an annotation history by pressing the '''show''' button in the cell '''annotation history''' some rows below. It will open a small table listing the date, the curator and the annotation that was made for each entry. As the genome name for the feature is already presented in the header of this section, we additionally show the '''taxonomy id''' for that genome in the overview. The link will lead to the Taxonomy Browser at the NCBI showing the taxonomy information for that genome. Behind the taxonomy for the genome you can find the '''contig''' the feature can be found on. The '''internal links''' you can see in the next row are leading to different pages containing other views and information for the feature. The [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] ('''genome browser''') displays the feature in the context of its genome. '''evidence''' leads to the [[SEED_Viewer_Manual/Evidence|Evidence]] page showing evidence for the annotation of the feature in form of Similarities and protein domains. Downloading the actual sequence for the feature is possible using the [[SEED_Viewer_Manual/ShowSeqs|Sequence Page]] ('''sequence''') link. Behind the external links you find a link to the '''ACH''' essentially identical genes. This link leads to the [[AnnotationClearingHouse|Annotation Clearing House]], a collection of proteins from many different sources. Proteins that have essentially the same sequence are grouped. For a given ID, you can see all IDs from different sources that belong to this group. At '''PubMed Links''' you can see the PubMed IDs to papers linked to the NCBI Entrez Database. The PubMed IDs shown are direct literature links attached directly to a feature, so-called '''dlits'''. '''FIGfams''' are protein families based on the subsystems technology. If you find an entry in this fields, the feature is part of the stated FIGfam. The link leads to the [[SEED_Viewer_Manual/FIGfams|FIGfam Viewer]]. '''database cross references''' link the feature to its entries (Aliases) in other databases like UniProt, GenBANK and many others. To gain more information about a feature, you can run different tools (e.g. PSI-BLAST, InterPro and many others) on your feature. Select a tool and press the button '''run tool'''. [[Image:AnnotationFeat.png]] === Reasons for Current Assignment === To gain a clue about what evidence an assignment of a functional role to your feature is based on, the text in '''Reasons for Current Assignment''' summarizes important information supporting the annotation. Additional to the information in the overview table, a list of indirect literature ('''ilits''') is decribed in the text. Those are based on direct literature to similar features that have the same functional role. [[Image:AnnotationAnnot.png]] === Compare Regions === The first line of the '''Compare Regions''' is a graphical display of the region of the feature its genome. All proteins are shown as colored arrows, where the direction depicts the strand of the feature. RNAs and other features are small boxes on the line. If two features overlap, the overlapping will be drawn on an (invisible) second line. The graph is centered on the selected feature (numbered 1), which is always colored red. Below you find the same region for orthologs in other (related) organisms, also colored in red. The colors of the other features (as well as the numbers) also represent ortholog (or sometimes also paralog) features. Whenever there are at least two ortholog or paralog features of a kind, a color (and a number) is assigned to them. '''Display Options''' are divided into two ''Regular'' and ''Advanced''. In the '''Regular''' options, you can change the ''Region Size'' and the ''Number of Regions''. Changing the '''Region Size''' enables to zoom in or out of the region. Changing the '''Number of Regions''' will add or remove genomes to your display. Click '''update graphics''' to change the display. The numbers that you put in for these values will be saved as [[SEED_Viewer_Manual/Preferences|preferences]]. [[Image:AnnotationComp.png]] If you click '''Advanced''' options, you will see the default options that are used for the Compare Regions View. The '''Pinned CDS Selection''' refers to the chosen peg and its orthologs in other genomes. The selection of genomes to show in the graphics can be made by ''Similarity'' or ''PCH pin''. The default is '''Similarity''' and means that the genomes are chosen using the similarity of the selected genes to its orthologs in other genomes. A '''PCH''' means a ''pair of close homologs''. [...] In the cell '''Genome Selection''' you can choose to ''collapse close genomes''. For many organism groups, the SEED database contains a number of strains that do not differ too strongly. They can be removed from the display using this option. The genomes in the display can be sorted by '''Phylogeny''' or '''Phylogenetic distance to input CDS'''. In the first case, the genome of the selected peg may not appear on the first line any more, but the genomes in the display are sorted by the overall phylogeny. The second (default) options will show the selected CDSs region on the first line and the other genomes in order of phylogenetic distance to the peg. The '''Evalue cutoff for selection of pinned CDSs''' depicts the minimum similarity CDSs may have to the selected CDS so that the its region is displayed. Defining if CDSs are orthologs or paralogs to a given CDS and therefore colored as such can be done using the '''Evalue cutoff for coloring CDS sets'''. We have implemented two different '''Coloring algorithms''' for the display. Default is a fast algorithm that might not always be absolutely accurate. You can choose a slower, but exact algorithm for coloring if you are unsure. [[Image:AnnotationAdv.png]] The second tab of the Compare Regions tab view lists all visible features in a table, sorted by the genome they appear in. The entries in the '''ID''' column link to the Annotation page of the feature. Additional to Start, Stop, Strand and Functional Role of the feature, you can see a column ''FC'', an ''SS'', a ''Set'' and a ''CL''. '''FC''' stands for ''[[Glossary#Functional Coupling|Functionally coupled]]'', showing the number of features that are coupled to this feature via clustering genomes or other evidence. The '''SS''' column shows the subsystems the feature is in. '''Set''' is the number that is depicted above a colored feature in the graphic. The '''cluster''' buttons in the last column leads to the [[SEED_Viewer_Manual/HomologClusters|Homolog clusters]] page for that feature. [[Image:AnnotationTabl.png]] 83d7af0c45bbdbaad1c820d34c880a81419d5797 0 1590 2347 2008-12-04T10:42:24Z DanielaBartels 10 wikitext text/x-wiki == FIGfams Release == Here you can find some statistics about FIGfams presented in a [[WebComponents/Tabview|TabView]]. The different tabs show you information about the '''Size Distribution''', the '''Subsystem Coverage''' and '''Quality Control''' of the FIGfams. === Size Distribution === This tab shows a graphic displaying the FIGfam Size against the FIGfam Quantity, for all releases of the FIGfams. For the latest release, you get a little table that tells you about the '''Version''', the '''Date''' the release was done, the number of FIGfams ('''FIGfams Quantity''') and the total number of sequences in FIGfams ('''Total Sequences'''). === Subsystem Coverage === The left bar in the graphics on this tab shows you the '''Subsystem Coverage''' of the FIGfams, meaning what percentage of the FIGfams is covered by subsystems. For these, you see a '''Category Distribution''' in the piechart in the middle. The tree right to the piechart lets you browse the categories shown in the piechart. For additional information how the use the graphics, see a similar graphic on the [[SEED_Viewer_Manual/OrganismPage|OrganismPage]]. === Quality Control === The third tab explains how Quality Control is made for the FIGfams using a small set of genomes. These are annotated using the FIGfams, and the annotations are compared against the current annotations of the genomes. 9e3f352ca7a8606a67c8e4d2dd9a8004273f8ce6 2349 2347 2008-12-04T10:44:36Z DanielaBartels 10 /* FIGfams Release */ wikitext text/x-wiki == FIGfams Release == Here you can find some statistics about FIGfams presented in a [[WebComponents/Tabview|TabView]]. The different tabs show you information about the '''Size Distribution''', the '''Subsystem Coverage''' and '''Quality Control''' of the FIGfams. === Size Distribution === This tab shows a graphic displaying the FIGfam Size against the FIGfam Quantity, for all releases of the FIGfams. For the latest release, you get a little table that tells you about the '''Version''', the '''Date''' the release was done, the number of FIGfams ('''FIGfams Quantity''') and the total number of sequences in FIGfams ('''Total Sequences'''). === Subsystem Coverage === The left bar in the graphics on this tab shows you the '''Subsystem Coverage''' of the FIGfams, meaning what percentage of the FIGfams is covered by subsystems. For these, you see a '''Category Distribution''' in the piechart in the middle. The tree right to the piechart lets you browse the categories shown in the piechart. For additional information how the use the graphics, see a similar graphic on the [[SEED_Viewer_Manual/OrganismPage#Subsystem Information|OrganismPage]]. === Quality Control === The third tab explains how Quality Control is made for the FIGfams using a small set of genomes. These are annotated using the FIGfams, and the annotations are compared against the current annotations of the genomes. fe333639dfa3c676017c39a52185df83e781d80d 0 1466 2348 2312 2008-12-04T10:43:44Z DanielaBartels 10 /* Main pages of the SeedViewer */ wikitext text/x-wiki == Main pages of the SeedViewer == '''[[SEED_Viewer_Manual|Home Page]]''' '''[[SEED_Viewer_Manual/Menu|Menu]]''' '''[[SEED_Viewer_Manual/Subsystems|Subsystems]]''' '''[[SEED_Viewer_Manual/FunctionalRoles|Functional Role]]''' '''[[SEED_Viewer_Manual/FIGfams|FIGfams]]''' '''[[SEED_Viewer_Manual/FIGfamViewer|FIGfam Viewer]]''' '''[[SEED_Viewer_Manual/FIGfamsRelease|FIGfam Release]]''' '''[[SEED_Viewer_Manual/Annotation|Annotation]]''' '''[[SEED_Viewer_Manual/Evidence|Evidence]]''' '''[[SEED_Viewer_Manual/BLASTOrganism|BLAST against an organism]]''' '''[[SEED_Viewer_Manual/ShowSeqs|Sequence]]''' '''[[SEED_Viewer_Manual/ContigView|Contig View]]''' '''[[SEED_Viewer_Manual/GenomeBrowser|Browse Genome]]''' '''[[SEED_Viewer_Manual/OrganismSelect|Organism Select]]''' '''[[SEED_Viewer_Manual/OrganismPage|Organism Page]]''' '''[[SEED_Viewer_Manual/KEGG|KEGG]]''' '''[[SEED_Viewer_Manual/HomologClusters|Homolog Clusters]]''' '''[[SEED_Viewer_Manual/CompareMetabolicReconstruction|Compare Metabolic Reconstruction]]''' '''[[SEED_Viewer_Manual/MultiGenomeCompare|Multi Genome Compare]]''' '''[[SEED_Viewer_Manual/BLASTDotPlot|BLAST Dot Plot]]''' '''[[SEED_Viewer_Manual/SearchGene|Search Gene]]''' '''[[SEED_Viewer_Manual/Scenarios|Scenarios]]''' 86b6f1bb4e2a47914ace542a20457ebf70e56d2f 2355 2348 2008-12-04T11:17:05Z DanielaBartels 10 /* Main pages of the SeedViewer */ wikitext text/x-wiki == Main pages of the SeedViewer == '''[[SEED_Viewer_Manual|Home Page]]''' '''[[SEED_Viewer_Manual/Menu|Menu]]''' '''[[SEED_Viewer_Manual/Annotation|Annotation]]''' '''[[SEED_Viewer_Manual/BLASTOrganism|BLAST against an organism]]''' '''[[SEED_Viewer_Manual/BLASTDotPlot|BLAST Dot Plot]]''' '''[[SEED_Viewer_Manual/GenomeBrowser|Browse Genome]]''' '''[[SEED_Viewer_Manual/CompareMetabolicReconstruction|Compare Metabolic Reconstruction]]''' '''[[SEED_Viewer_Manual/ContigView|Contig View]]''' '''[[SEED_Viewer_Manual/Evidence|Evidence]]''' '''[[SEED_Viewer_Manual/FIGfams|FIGfams]]''' '''[[SEED_Viewer_Manual/FIGfamsRelease|FIGfam Release]]''' '''[[SEED_Viewer_Manual/FIGfamViewer|FIGfam Viewer]]''' '''[[SEED_Viewer_Manual/FunctionalRoles|Functional Role]]''' '''[[SEED_Viewer_Manual/HomologClusters|Homolog Clusters]]''' '''[[SEED_Viewer_Manual/KEGG|KEGG Page]]''' '''[[SEED_Viewer_Manual/MultiGenomeCompare|Multi Genome Compare]]''' '''[[SEED_Viewer_Manual/OrganismPage|Organism Page]]''' '''[[SEED_Viewer_Manual/OrganismSelect|Organism Select]]''' '''[[SEED_Viewer_Manual/SearchGene|Search Gene]]''' '''[[SEED_Viewer_Manual/Scenarios|Scenarios]]''' '''[[SEED_Viewer_Manual/ShowSeqs|Sequence]]''' '''[[SEED_Viewer_Manual/Subsystems|Subsystems]]''' 78cc7af444c61655855546f6cf03bf6b8f2a7fcb 2356 2355 2008-12-04T11:17:19Z DanielaBartels 10 /* Main pages of the SeedViewer */ wikitext text/x-wiki == Main pages of the SeedViewer == '''[[SEED_Viewer_Manual|Home Page]]''' '''[[SEED_Viewer_Manual/Menu|Menu]]''' '''[[SEED_Viewer_Manual/Annotation|Annotation]]''' '''[[SEED_Viewer_Manual/BLASTOrganism|BLAST against an organism]]''' '''[[SEED_Viewer_Manual/BLASTDotPlot|BLAST Dot Plot]]''' '''[[SEED_Viewer_Manual/GenomeBrowser|Browse Genome]]''' '''[[SEED_Viewer_Manual/CompareMetabolicReconstruction|Compare Metabolic Reconstruction]]''' '''[[SEED_Viewer_Manual/ContigView|Contig View]]''' '''[[SEED_Viewer_Manual/Evidence|Evidence]]''' '''[[SEED_Viewer_Manual/FIGfams|FIGfams]]''' '''[[SEED_Viewer_Manual/FIGfamsRelease|FIGfam Release]]''' '''[[SEED_Viewer_Manual/FIGfamViewer|FIGfam Viewer]]''' '''[[SEED_Viewer_Manual/FunctionalRoles|Functional Role]]''' '''[[SEED_Viewer_Manual/HomologClusters|Homolog Clusters]]''' '''[[SEED_Viewer_Manual/KEGG|KEGG Page]]''' '''[[SEED_Viewer_Manual/MultiGenomeCompare|Multi Genome Compare]]''' '''[[SEED_Viewer_Manual/OrganismPage|Organism Page]]''' '''[[SEED_Viewer_Manual/OrganismSelect|Organism Select]]''' '''[[SEED_Viewer_Manual/SearchGene|Search Gene]]''' '''[[SEED_Viewer_Manual/Scenarios|Scenarios]]''' '''[[SEED_Viewer_Manual/ShowSeqs|Sequence]]''' '''[[SEED_Viewer_Manual/Subsystems|Subsystems Page]]''' 45792462ab586782c9c6bfeaf8d7720cee3fada6 2357 2356 2008-12-04T11:33:17Z DanielaBartels 10 /* Main pages of the SeedViewer */ wikitext text/x-wiki == Main pages of the SeedViewer == '''[[SEED_Viewer_Manual|Home Page]]''' '''[[SEED_Viewer_Manual/Menu|Menu]]''' '''[[SEED_Viewer_Manual/Annotation|Annotation]]''' '''[[SEED_Viewer_Manual/BLASTOrganism|BLAST against an organism]]''' '''[[SEED_Viewer_Manual/BLASTDotPlot|BLAST Dot Plot]]''' '''[[SEED_Viewer_Manual/DownloadOrganism|Download Organism]]''' '''[[SEED_Viewer_Manual/GenomeBrowser|Browse Genome]]''' '''[[SEED_Viewer_Manual/CompareMetabolicReconstruction|Compare Metabolic Reconstruction]]''' '''[[SEED_Viewer_Manual/ContigView|Contig View]]''' '''[[SEED_Viewer_Manual/Evidence|Evidence]]''' '''[[SEED_Viewer_Manual/FIGfams|FIGfams]]''' '''[[SEED_Viewer_Manual/FIGfamsRelease|FIGfam Release]]''' '''[[SEED_Viewer_Manual/FIGfamViewer|FIGfam Viewer]]''' '''[[SEED_Viewer_Manual/FunctionalRoles|Functional Role]]''' '''[[SEED_Viewer_Manual/HomologClusters|Homolog Clusters]]''' '''[[SEED_Viewer_Manual/KEGG|KEGG Page]]''' '''[[SEED_Viewer_Manual/MultiGenomeCompare|Multi Genome Compare]]''' '''[[SEED_Viewer_Manual/OrganismPage|Organism Page]]''' '''[[SEED_Viewer_Manual/OrganismSelect|Organism Select]]''' '''[[SEED_Viewer_Manual/SearchGene|Search Gene]]''' '''[[SEED_Viewer_Manual/Scenarios|Scenarios]]''' '''[[SEED_Viewer_Manual/ShowSeqs|Sequence]]''' '''[[SEED_Viewer_Manual/Subsystems|Subsystems Page]]''' 793d4a278c6742f21dc92bd57c14a4d92273ecc5 2380 2357 2008-12-05T09:53:46Z DanielaBartels 10 /* Main pages of the SeedViewer */ wikitext text/x-wiki == Main pages of the SeedViewer == '''[[SEED_Viewer_Manual|Home Page]]''' '''[[SEED_Viewer_Manual/Menu|Menu]]''' '''[[SEED_Viewer_Manual/Annotation|Annotation]]''' '''[[SEED_Viewer_Manual/AlignSeqs|Alignment Page]]''' '''[[SEED_Viewer_Manual/BLASTOrganism|BLAST against an organism]]''' '''[[SEED_Viewer_Manual/BLASTDotPlot|BLAST Dot Plot]]''' '''[[SEED_Viewer_Manual/DownloadOrganism|Download Organism]]''' '''[[SEED_Viewer_Manual/GenomeBrowser|Browse Genome]]''' '''[[SEED_Viewer_Manual/CompareMetabolicReconstruction|Compare Metabolic Reconstruction]]''' '''[[SEED_Viewer_Manual/ContigView|Contig View]]''' '''[[SEED_Viewer_Manual/Evidence|Evidence]]''' '''[[SEED_Viewer_Manual/FIGfams|FIGfams]]''' '''[[SEED_Viewer_Manual/FIGfamsRelease|FIGfam Release]]''' '''[[SEED_Viewer_Manual/FIGfamViewer|FIGfam Viewer]]''' '''[[SEED_Viewer_Manual/FunctionalRoles|Functional Role]]''' '''[[SEED_Viewer_Manual/HomologClusters|Homolog Clusters]]''' '''[[SEED_Viewer_Manual/KEGG|KEGG Page]]''' '''[[SEED_Viewer_Manual/MultiGenomeCompare|Multi Genome Compare]]''' '''[[SEED_Viewer_Manual/OrganismPage|Organism Page]]''' '''[[SEED_Viewer_Manual/OrganismSelect|Organism Select]]''' '''[[SEED_Viewer_Manual/SearchGene|Search Gene]]''' '''[[SEED_Viewer_Manual/Scenarios|Scenarios]]''' '''[[SEED_Viewer_Manual/ShowSeqs|Sequence]]''' '''[[SEED_Viewer_Manual/Subsystems|Subsystems Page]]''' debc1c46c37686bba63fb908da895c49c369dd48 0 1591 2350 2008-12-04T11:08:48Z DanielaBartels 10 wikitext text/x-wiki == Request New Password == If you have a login, but you forgot your password, you can use this page to get a new one. Type in your user login and your email address, and press the button '''Request new password'''. The system will check if your login fits to your email (meaning that you have to use the same email as you did when requesting the account). If you cannot access your email any more, you have to contact the SEED team using the '''Contact''' link in the '''[[SEED_Viewer_Manual/Menu#Help Menu|Help Menu]]'''. [[Image:RequestPassword.png]] 20ade930e4187bff66500203ca5a9f3ab9d31291 2351 2350 2008-12-04T11:09:19Z DanielaBartels 10 /* Request New Password */ wikitext text/x-wiki == Request New Password == If you have a login, but you forgot your password, you can use this page to get a new one. Type in your user login and your email address, and press the button '''Request new password'''. The system will check if your login fits to your email (meaning that you have to use the same email as you did when requesting the account). If you cannot access your email any more, you have to contact the SEED team using the '''Contact''' link in the '''[[SEED_Viewer_Manual/Menu#Help Menu|Help Menu]]''' for help. [[Image:RequestPassword.png]] 3d3d661801c50820ad2a4d05afc2bc8113a4d0f3 2352 2351 2008-12-04T11:12:05Z DanielaBartels 10 /* Request New Password */ wikitext text/x-wiki == Request New Password == If you have a login, but you forgot your password, you can use this page to get a new one. Type in your user login and your email address, and press the button '''Request new password'''. The system will check if your login fits to your email (meaning that you have to use the same email as you did when requesting the account). It will then send you a new cryptic password, which you should immediately change using the [[SEED_Viewer_Manual/UserManagement|User Management]] link (for more information see [[WebComponents/Login|here]]. If you cannot access your email any more, you have to contact the SEED team using the '''Contact''' link in the '''[[SEED_Viewer_Manual/Menu#Help Menu|Help Menu]]''' for help. [[Image:RequestPassword.png]] 8d3550a8355fd3ae8b7ad0a416d55974aefe587e 2353 2352 2008-12-04T11:12:22Z DanielaBartels 10 /* Request New Password */ wikitext text/x-wiki == Request New Password == If you have a login, but you forgot your password, you can use this page to get a new one. Type in your user login and your email address, and press the button '''Request new password'''. The system will check if your login fits to your email (meaning that you have to use the same email as you did when requesting the account). It will then send you a new cryptic password, which you should immediately change using the [[SEED_Viewer_Manual/UserManagement|User Management]] link (for more information see [[WebComponents/Login|here]]). If you cannot access your email any more, you have to contact the SEED team using the '''Contact''' link in the '''[[SEED_Viewer_Manual/Menu#Help Menu|Help Menu]]''' for help. [[Image:RequestPassword.png]] 37a45413ff40d99bcf197d96c670f0afee280a5a 6 1592 2354 2008-12-04T11:12:39Z DanielaBartels 10 wikitext text/x-wiki da39a3ee5e6b4b0d3255bfef95601890afd80709 0 1478 2358 2315 2008-12-04T11:33:47Z DanielaBartels 10 /* Organism Menu */ wikitext text/x-wiki == Menu Overview == The menu is a small bar below the logo of each page. Most menus have submenus that can be accessed via hovering over the menu. Right-click the submenu you want to go to. If no submenu is present, you can directly click the menu itself. === Navigate Menu === This menu is present on every SeedViewer page. The first entry '''Startpage''' will lead to the SeedViewer [[SEED_Viewer_Manual|HomePage]]. '''Organisms''' will open the [[SEED_Viewer_Manual/OrganismSelect|Organism Select]] page. You will see an overview of all organisms in the SEED and are able to select one to view in detail. '''Subsystems''' will do the same for subsystems. '''Scenarios''' lets you browse [[Glossary#Scenarios|Scenarios]] on the [[SEED_Viewer_Manual/Scenarios|Scenarios Page]]. '''FIGFams''' leads to an entry point for browsing [[SEED_Viewer_Manual/FIGfams|FIGfams]]. You can find more information about FIGfams [[Glossary#FIGfam|here]]. The '''BLAST Search''' links to the [[SEED_Viewer_Manual/BLASTOrganism|BLAST Page]]. You will be able to BLAST a sequence against an organism in the SEED. [[Image:MenuNav.png]] === Help Menu === This menu is also present on all SeedViewer pages. The first link '''What is the SEED''' will lead you to the [[Home_of_the_SEED|SEED Homepage]]. Clicking the second link '''How to use the SEED Viewer''' will get you to this wiki. '''Submitting data to SEED''' lets you browse the [[RAST_Tutorial|RAST Tutorial]]. '''Contact''' enables you to write an email to the SEED team. Clicking '''Register''' is the first step to get a user account. It will lead to the [[SEED_Viewer_Manual/Register|Register]] page. '''I forgot my password''' enables you to [[SEED_Viewer_Manual/RequestNewPassword|Request a new password]]. [[Image:MenuHelp.png]] === Organism Menu === In the context of a selected organism, an organism menu will appear. '''General Information''' will lead to the [[SEED_Viewer_Manual/OrganismPage|Organism Page]] of the selected organism. The '''Feature Table''' will open the [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] and show you the features present in that organism. '''Genome Browser''' leads to the [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] for the selected organism. Clicking '''Scenarios''' shows the [[SEED_Viewer_Manual/Scenarios|Scenarios]] page for your organism. '''Subsystems''' opens a page that lets you select subsystems. '''Export''' enables you to [[SEED_Viewer_Manual/DownloadOrganism|download]] the features of your organism. [[Image:MenuOrganism.png]] === Comparative Tools === This menu is also present whenever an organism is viewed. Different kinds of comparisons of your selected organism to other organisms are available here. '''Function based Comparison''' - The [[SEED_Viewer_Manual/CompareMetabolicReconstruction|Compare Metabolic Reconstruction]] will enable you to see the metabolic reconstruction of your selected organism against that of another one. The '''Sequence based Comparison''' [[SEED_Viewer_Manual/MultiGenomeCompare|Multi Genome Compare]] shows a table and a graphics comparing a selected set of organisms projected against your chosen one (BLAST-based). Use the '''KEGG Metabolic Analysis''' [[SEED_Viewer_Manual/KEGG|to project the metabolic capabilities]] of your organism on KEGG maps. Blasting against your organism is enabled using the '''[[SEED_Viewer_Manual/BLASTOrganism|BLAST Search]]'''. [[Image:CompTools.png]] === Feature Menu === Whenever a feature is defined on a SeedViewer page, you will find the '''Feature''' menu for that feature. The '''Feature Overview''' points to the [[SEED_Viewer_Manual/Annotation|Annotation]] page. It shows general information about the feature, als well as a Compare Regions View that displays the feature in its genomic context and in comparison to homologs in other genomes. '''DNA Sequence''' will open a page with the DNA Sequence of the feature (in FASTA format). '''DNA w/ flanking''' not only prints the DNA sequence of the feature, but also includes a user-defined number of bases upstream and downstream of the feature. '''Protein Sequence''' will show you the protein FASTA sequence (translated from the DNA sequence) of the feature. '''Feature Evidence vs. FIG''' and '''Feature Evidence vs. all DB''' link to the [[SEED_Viewer_Manual/Evidence|Evidence]] page. The difference between the two is that the evidence shown for the feature includes only evidence against features in the SEED or also against other databases (e.g. GenBank, SwissProt, UniProt and many others). The evidence page will also allow you to make this selection or change it there. [[Image:MenuFeature.png]] === Feature Tools === This menu is also present if a feature is defined. It lets the user run a variaty of tools using the feature sequence. These include tools that look for transmembrane helices (e.g. [http://www.cbs.dtu.dk/services/TMHMM/ TMHMM]), signal peptides ([http://www.psort.org/ PSORT], [http://www.cbs.dtu.dk/services/SignalP/ SignalP]), protein domains (e.g. [http://www.ebi.ac.uk/interpro/ InterPro], [http://prodom.prabi.fr/prodom/current/html/home.php ProDom]) and others. [[Image:MenuFeatTools.png]] === FIGfams Menu === On SeedViewer pages that deal with [[Glossary#FIGfam|FIGfams]], you will find an additional FIGfams menu. The '''Home''' link leads to the entry page to [[SEED_Viewer_Manual/FIGfams|FIGfams]]. The '''Release History''' will lead you to a [[SEED_Viewer_Manual/FIGfamsRelease|page]] containing a number of statistics about the current release of the FIGfams. '''Download''' will connect you to the FTP server to enable you to download the FIGfams. [[Image:MenuFIGfam.png]] b2f6b917b4947b8d2933d17109c64b84e2eb2135 6 1593 2361 2008-12-04T13:49:14Z DanielaBartels 10 wikitext text/x-wiki da39a3ee5e6b4b0d3255bfef95601890afd80709 6 1594 2362 2008-12-04T13:49:40Z DanielaBartels 10 wikitext text/x-wiki da39a3ee5e6b4b0d3255bfef95601890afd80709 0 1595 2365 2008-12-04T14:42:05Z DanielaBartels 10 wikitext text/x-wiki == Editing Capabilities - Annotation Page == [[Image:AnnotationEdit.png]] 1f2b3b991ff725ea32dadcab36f3b8432ed306ad 2367 2365 2008-12-04T14:51:39Z DanielaBartels 10 /* Editing Capabilities - Annotation Page */ wikitext text/x-wiki == Editing Capabilities - Annotation Page == If you have the right to edit the feature for which the [[SEED_Viewer_Manual/Annotation|Annotation Page]] is displayed, you will get two additional fields in the Annotation Overview, '''new assignment''' and '''comment'''. To annotate a feature, you can simply put the new assignment into the text field at the '''new assignment'''. Note that the annotation can be a combination of functional roles. Functional roles can be combined to an assignment using different separators: ' / ' separates two functional roles that refer to different parts of the feature. This separator is for example used for fusion genes, or multi-domain proteins where different domains implement those functional roles. [[Image:AnnotationEdit.png]] 5558fc02061a4ea3f4d11a81ba55dde5c3a0211f 2368 2367 2008-12-04T14:59:10Z DanielaBartels 10 /* Editing Capabilities - Annotation Page */ wikitext text/x-wiki == Editing Capabilities - Annotation Page == If you have the right to edit the feature for which the [[SEED_Viewer_Manual/Annotation|Annotation Page]] is displayed, you will get two additional fields in the Annotation Overview, '''new assignment''' and '''comment'''. To annotate a feature, you can simply put the new assignment into the text field at the '''new assignment'''. Note that the annotation can be a combination of functional roles. Functional roles can be combined to an assignment using different separators: ' / ' separates two functional roles that refer to different parts of the feature. This separator is for example used for fusion genes, or multi-domain proteins where different domains implement those functional roles. ' @ ' also separates different functional roles for one protein, but the functions refer to the same part of the protein. This is used if a domain or a part of the protein can implement both functions in different contexts. ' ; ' is used if you are unsure which of the functions a protein implements. ' # ' is followed by a text that is added as a comment to the functional role. This is for example used for marking features as truncated. After typing in your new functional assignment to your feature, press '''change''' to make the annotation. Another option that you have access to if you can edit the feature is deleting it. If you are sure that the feature should be deleted, press the button '''delete feature'''. The system will ask you again if you really want to delete the feature, to prevent people from accidently deleting features. [[Image:AnnotationEdit.png]] 2c5ac1b48992c9a3f0ef8e34e6b18be468edd97a 2369 2368 2008-12-04T15:08:03Z DanielaBartels 10 /* Editing Capabilities - Annotation Page */ wikitext text/x-wiki == Editing Capabilities - Annotation Page == If you have the right to edit the feature for which the [[SEED_Viewer_Manual/Annotation|Annotation Page]] is displayed, you will get two additional fields in the Annotation Overview, '''new assignment''' and '''comment'''. To annotate a feature, you can simply put the new assignment into the text field at the '''new assignment'''. Note that the annotation can be a combination of functional roles. Functional roles can be combined to an assignment using different separators: ' / ' separates two functional roles that refer to different parts of the feature. This separator is for example used for fusion genes, or multi-domain proteins where different domains implement those functional roles. ' @ ' also separates different functional roles for one protein, but the functions refer to the same part of the protein. This is used if a domain or a part of the protein can implement both functions in different contexts. ' ; ' is used if you are unsure which of the functions a protein implements. ' # ' is followed by a text that is added as a comment to the functional role. This is for example used for marking features as truncated. If you'd like to give additional comments to your annotation, the '''comment''' textbox is the right place for this. After typing in your new functional assignment to your feature, press '''change''' to make the annotation. Another option that you have access to if you can edit the feature is deleting it. If you are sure that the feature should be deleted, press the button '''delete feature'''. The system will ask you again if you really want to delete the feature, to prevent people from accidently deleting features. '''curate literature''' leads to a page where you can add direct literature links (dlits) to a feature. Press [[SEED_Viewer_Manual/EditLiterature|here]] to get more information. [[Image:AnnotationEdit.png]] f2dd464088e6a1679ebd99d2193c348136ecc5bf 6 1596 2366 2008-12-04T14:42:39Z DanielaBartels 10 wikitext text/x-wiki da39a3ee5e6b4b0d3255bfef95601890afd80709 0 1597 2370 2008-12-04T15:35:21Z DanielaBartels 10 wikitext text/x-wiki == Edit Literature == This page allows you to edit direct literature (dlits) for a feature. The tool automatically queries PubMed for Aliases of the feature ID to get candidate literatures for your feature. === CDS Info === This section displays a table with general information for the feature that might be valuable for deciding if a literature reference is relevant for the feature. === Requesting relevant publications from PubMed === === Curating literature in SEED === '''1) Add additional publications for this peg''' '''2) Drag and drop the PMID to the appropriate containers.''' 3cb805be7a8c45b1590b2694bff4859373b570cf 2371 2370 2008-12-04T15:43:00Z DanielaBartels 10 /* Requesting relevant publications from PubMed */ wikitext text/x-wiki == Edit Literature == This page allows you to edit direct literature (dlits) for a feature. The tool automatically queries PubMed for Aliases of the feature ID to get candidate literatures for your feature. === CDS Info === This section displays a table with general information for the feature that might be valuable for deciding if a literature reference is relevant for the feature. === Requesting relevant publications from PubMed === This section displays publications that are not yet curated, as well as publications that are already assigned to be relevant or not relevant to the function of the feature. Not yet Curated relevant publications: === Curating literature in SEED === '''1) Add additional publications for this peg''' '''2) Drag and drop the PMID to the appropriate containers.''' a23de957d63a5b48f15f7b52e2f317928adfd21c 2372 2371 2008-12-04T16:18:31Z DanielaBartels 10 /* Requesting relevant publications from PubMed */ wikitext text/x-wiki == Edit Literature == This page allows you to edit direct literature (dlits) for a feature. The tool automatically queries PubMed for Aliases of the feature ID to get candidate literatures for your feature. === CDS Info === This section displays a table with general information for the feature that might be valuable for deciding if a literature reference is relevant for the feature. === Requesting relevant publications from PubMed === This section displays publications that are not yet curated, as well as publications that are already assigned to be relevant or not relevant to the function of the feature. The literature references appear in the following tables: '''Not yet Curated relevant publications:''' These are publications the tool has identified as possibly relevant for the feature. You will get a checkbox in the first column of the table. Check the publications you want to assign as supporting the functional assignment of the feature, and press the button '''Save to relevant pmids''' underneath the table to save them as dlits. '''Not yet curated publications (dlits):''' Same as above, but the literature references were pre-computed. '''Current DLITS for this gene:''' This table shows all publications that are assigned to support the functional assignment of the feature (to be dlits). '''Curated to be RELEVANT, but NOT DLITS:''' Literature that is relevant, but not a dlit is literature that does not support the functional assignment to the feature, but refer to the genomic region the feature is in or give other information about the feature. '''Curated to be GENOME PAPERS, not dlits:''' These are references that refer to the whole genome of the feature or a genomic region, not directly the feature itself. Mostly, these papers deal with the sequencing process of the genome. '''Curated to be NOT RELEVANT publications:''' Not relevant publications. === Curating literature in SEED === '''1) Add additional publications for this peg''' '''2) Drag and drop the PMID to the appropriate containers.''' 63b6509681640cb3d480b071b362f7e23625dce4 2373 2372 2008-12-04T16:39:19Z DanielaBartels 10 /* Curating literature in SEED */ wikitext text/x-wiki == Edit Literature == This page allows you to edit direct literature (dlits) for a feature. The tool automatically queries PubMed for Aliases of the feature ID to get candidate literatures for your feature. === CDS Info === This section displays a table with general information for the feature that might be valuable for deciding if a literature reference is relevant for the feature. === Requesting relevant publications from PubMed === This section displays publications that are not yet curated, as well as publications that are already assigned to be relevant or not relevant to the function of the feature. The literature references appear in the following tables: '''Not yet Curated relevant publications:''' These are publications the tool has identified as possibly relevant for the feature. You will get a checkbox in the first column of the table. Check the publications you want to assign as supporting the functional assignment of the feature, and press the button '''Save to relevant pmids''' underneath the table to save them as dlits. '''Not yet curated publications (dlits):''' Same as above, but the literature references were pre-computed. '''Current DLITS for this gene:''' This table shows all publications that are assigned to support the functional assignment of the feature (to be dlits). '''Curated to be RELEVANT, but NOT DLITS:''' Literature that is relevant, but not a dlit is literature that does not support the functional assignment to the feature, but refer to the genomic region the feature is in or give other information about the feature. '''Curated to be GENOME PAPERS, not dlits:''' These are references that refer to the whole genome of the feature or a genomic region, not directly the feature itself. Mostly, these papers deal with the sequencing process of the genome. '''Curated to be NOT RELEVANT publications:''' Not relevant publications. === Curating literature in SEED === Curation of the literature can be done two ways: '''1) Add additional publications for this peg''' You can manually add publications that have not appeared in any of the tables above. If you want to add more than one PubMed reference, separate them with a space. Press '''Save to relevant pmids''' to save the entered publications as supporting the functional assignment of the feature (dlit). '''2) Drag and drop the PMID to the appropriate containers.''' The categories for the publications described above can be found as containers in this section. The literature boxes in the containsers can be dragged and dropped from one container to another. This way, you can move any of the literature references to any container. If you have made your selection, press '''Save to attributes''' to save your selection. aa8f31ffce5c2867501d52a668be43a9737a9307 0 1565 2374 2270 2008-12-04T16:40:21Z DanielaBartels 10 /* Editing capabilities in the SeedViewer */ wikitext text/x-wiki == Editing capabilities in the SeedViewer == [[SEED_Viewer_Manual/Editing_Capabilities/Annotation|Annotation Page]] [[SEED_Viewer_Manual/Editing_Capabilities/ChromosomalClusters|Chromosomal Clusters Page]] [[SEED_Viewer_Manual/Editing_Capabilities/Evidence|Evidence Page]] [[SEED_Viewer_Manual/Editing_Capabilities/SearchGene|Search Gene Page]] [[SEED_Viewer_Manual/Editing_Capabilities/EditLiterature|Edit Literature for a feature]] 5529c83d566d993d8d3c8f9ccfa570e3e43ea627 2375 2374 2008-12-04T16:41:26Z DanielaBartels 10 /* Editing capabilities in the SeedViewer */ wikitext text/x-wiki == Editing capabilities in the SeedViewer == [[SEED_Viewer_Manual/Editing_Capabilities/Annotation|Annotation Page]] [[SEED_Viewer_Manual/Editing_Capabilities/ChromosomalClusters|Chromosomal Clusters Page]] [[SEED_Viewer_Manual/Editing_Capabilities/Evidence|Evidence Page]] [[SEED_Viewer_Manual/Editing_Capabilities/SearchGene|Search Gene Page]] [[SEED_Viewer_Manual/EditLiterature|Edit Literature for a feature]] bb62b2ae959e5979196d9902a6a4dc65dc8fb71a 0 1598 2376 2008-12-05T09:21:18Z DanielaBartels 10 wikitext text/x-wiki == Editing Capabilities - Annotation Page == cfddc70d636524b5a9bd2de4f9d4ddb928af4baa 2377 2376 2008-12-05T09:50:41Z DanielaBartels 10 /* Editing Capabilities - Annotation Page */ wikitext text/x-wiki == Editing Capabilities - Evidence Page == If you have the right to edit the feature for which the [[SEED_Viewer_Manual/Evidence|Evidence Page]] is displayed, there will be some additional options visible. 07b2b989b344ef396c46902f49872894dab9f3a2 2381 2377 2008-12-05T09:55:24Z DanielaBartels 10 /* Editing Capabilities - Evidence Page */ wikitext text/x-wiki == Editing Capabilities - Evidence Page == If you have the right to edit the feature for which the [[SEED_Viewer_Manual/Evidence|Evidence Page]] is displayed, there will be some additional options visible. [[Image:EditEvidence.png]] 466888c530d0376f848c1baf2a9279d967bd5b1e 2382 2381 2008-12-05T09:56:37Z DanielaBartels 10 /* Editing Capabilities - Evidence Page */ wikitext text/x-wiki == Editing Capabilities - Evidence Page == If you have the right to edit the feature for which the [[SEED_Viewer_Manual/Evidence|Evidence Page]] is displayed, there will be some additional options visible in the ''[[SEED_Viewer_Manual/Evidence#Tabular Protein Evidence|Tabular Protein Evidence tab]]''. [[Image:EditEvidence.png]] 961ca5faea930edea6e32d162fec0b055abe890e 0 1502 2378 2100 2008-12-05T09:52:05Z DanielaBartels 10 /* Similarities */ wikitext text/x-wiki The Evidence Page is divided into two parts via a [[WebComponents/Tabview|TabView]]: The '''Visual Protein Evidence''' and the '''Tabular Protein Evidence'''. If you are logged in and the feature belongs to your private genome, this page will have additional options for you to annotate the feature. These are described [[SEED_Viewer_Manual/Editing_Capabilities/Evidence|here]]. == Visual Protein Evidence == After loading the Evidence Page, the first tab of the [[WebComponent/Tabview|TabView]] is selected. It visually shows different pre-computed tool results for the given feature. In this view, you can see evidence for ''Location'' of the product of the gene in the cell, evidence for protein ''Domains'' and evidence that show ''Similarities'' to other features. === Location === '''Location''' stand for location of the product of the feature in the cell. This section presents output for tools that look for transmembrane helices (TM) or signal peptides (SP) in the feature. In the example, you can see five transmembrane helices in the protein identified via the Phobius tool. They are visualized as little boxes, and their location on the line depicts the location of the transmembrane helices in the protein. [[Image:EvidenceLocation.png]] === Domains === This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the full length of the protein). Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]]''' in the menu bar. [[Image:EvidenceDomain.png]] === Similarities === This section graphically lists evidence for similarities to other features in the SEED and other databases. The '''E-Value Key''' shown on the top defines the colors that are used to display different E-Value ranges for the similarities to the hit features. Hovering over the E-Value Key shows the value range for each color. Each similarity is represented by two bars, showing the alignment of the similarity. The first bar is the '''query''' feature, the second the '''hit''' feature. The abbreviation in front of this bar informs you about the organism the hit feature is in. Hover over the abbreviation to get the complete organism name. To the right of the checkbox you can find the [[Glossary#Functional role|functional role]] of the hit feature. The length of the outside box shows the complete length of the respective sequence. The color of the outside box represents the range of the evalue score according to the E-Value Key bar. The length of the inner (white) box depicts the actual section of the sequence the similarity to the other feature is in. Hovering over the box will show you some information about the hit feature (see tooltip graphics below), including the [[Glossary#Functional role|functional role]], the [[Glossary#Subsystem|subsystems]] and some values describing the hit area. If you check some of the checkboxes in front of the [[Glossary#Functional role|functional role]] descriptions of the hit genes, you can access two functions via the buttons on top of the Similarity graphics. The button '''Align Selected''' leads to an [[SEED_Viewer_Manual/AlignSeqs|alignment page]] showing a TCoffee alignment for the selected features. '''FASTA Download Selected''' lets you download the selected sequences in aminoacid FASTA format. [[Image:EvidenceSims1.png]] [[Image:EvidenceHoverSim.png]] To change the evidence view with respect to the sorting and the filtering of the hits, you can find a little control box on top of the similarity graphics. '''Max Sims''' is the number of similarities that are listed on the page. '''Max E-Value''' filters out all similarities that have a higher E-Value than stated here. In the little combo box below these two values, you can decide to see only hits against the SEED database ('''Just FIG IDs'''), or also against other databases ('''Show all Databases'''). You can '''Sort''' the '''Results By''' ''Score'', ''Percent Identity'' (default) or ''Score per position''. These values locally refer to the hit as known from BLAST hits, so a high percent identity referring to a very small hit region can make this similarity show up as one of the first hits, as shown in the example. Checking '''Group by Genome''' will aggregate all hits to features in the same genome. A blue box will mark hits that belong to the same genome. After selecting the right values, you can press the button '''Resubmit''' to change the evidence view. [[Image:EvidenceFil1.png]] == Tabular Protein Evidence == Activate the second tab of the large page-spanning [[WebComponents/Tabview|TabView]] to see the tabular view of the evidence. You will find most of the information already shown in the visual view, presented differently and enriched with some additional information. Added are the '''Identical Proteins''' and the '''Functionally coupled''' sections, while '''Location''' information is not presented in this tab. === Similarities === The similarity [[WebComponents/Table|table]] lists hits to similar features in the SEED and other databases, as described at [[SEED_Viewer_Manual/Evidence#Visual Protein Evidence|Visual Protein Evidence]]. Each row in the table represents a hit. The first column provides a checkbox to select a hit feature. Again, the buttons '''Align Selected''' and '''FASTA Download Selected''' are present and can be used to get to a TCoffee [[SEED_Viewer_Manual/AlignSeqs|alignment page]] or download the protein sequences of the selected features in FASTA format. The two buttons in the column header allow mass selection of the features. '''All''' will select all features visible in the table, '''check to last checked''' lets you select all features up to a selected feature in the [[WebComponents/Table|table]]. The ID of the hit features, as well as a link to the [[SEED_Viewer_Manual/Annotation|annotation page]] is displayed in the column '''Similar FIG Sequence'''. The next four columns describe information to the hit regions of the query and hit features ('''E-value''', '''Percent Identity''', '''Region in Query peg''' and '''Region in Similar Sequence'''). The '''Organism''' of the hit peg and its '''Function''' are shown in the next two columns. If the function is different from the function of the query feature, it is colored. Same function in the table will get the same color. '''Associated Subsystems'' of the feature are displayed in the next column. If the feature is not associated to a subsystem, you will find the text ''None added'' in the cell. There are three '''Evidence Codes''' that can be found in the last column. ''ISU'' means that the feature is unique in a cell of a subsystem. This means that there is no other feature in the genome that is thought to have the same function. ICW(number) means the feature is clustered with ''number'' features in the genome. ''FF'' says that it is in a [[Glossary#FIGfam|FIGfam]]. The [[WebComponents/Table|table]] can be exported via the button '''export table''' that can be found on top of the table. [[Image:EvidenceSims2.png]] You can filter and sort the table using the [[WebComponents/Tabview|TabView]] above the table. The second tab, '''Sims Filter''' works the same way as described for the Similarities in the [[SEED_Viewer_Manual/Evidence#Visual Protein Evidence|Visual Protein Evidence]]. The first tab '''Edit Columns''' contains a number of columns with additional information that can be added to the display of the table ([[Glossary#FIGfams|FIGfams]], different aliases to other databases and many others). Just choose a column name, press the arrow to put it into the right field and it will add it to the table. [[Image:EvidenceFilter.png]] === Domains === This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the whole length of the protein). The [[WebComponents/Table|table]] lists the '''Domain DB''' (the database for the domain that was hit), the '''ID''' in the domain database, the '''Name''' of the domain, the '''Location''' of the hit in the selected feature, the '''Score''' for the hit against the domain, as well as the '''Function''' of the domain. The table can be exported using the '''export table''' button. Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]]''' in the menu bar. [[Image:EvidenceDomTable.png]] === Identical Proteins === '''Essentially Identical Proteins''' are proteins that share a common sequence, but the start position of the proteins may vary a little. This definition was made because in different databases or close strains of organisms, it often happens that a protein is present, but the start position may be shifted in the finding genes step. So essentially, this table shows aliases of the feature that were based on protein identity. The first column of the [[WebComponents/Table|table]] shows the '''Database''' the alias can be found in, while the second column ('''ID''') offers the alias name and a link to the protein in the respective database. The following two columns describe the '''Organism''' and the '''Assignment''' for the feature for the alias. [[Image:EvidenceEIPs.png]] === Functionally Coupled === This [[WebComponent/Table|table]] lists all [[Glossary#Functional coupling|functionally coupled]] genes in the organism. You can see the '''Score''', the '''ID''' of the feature and the '''Function''' of the feature. [[Image:EvidenceFCs.png]] 6fb95c89a5a749dc79df5278519a1000ebcf4994 2379 2378 2008-12-05T09:52:35Z DanielaBartels 10 /* Functionally Coupled */ wikitext text/x-wiki The Evidence Page is divided into two parts via a [[WebComponents/Tabview|TabView]]: The '''Visual Protein Evidence''' and the '''Tabular Protein Evidence'''. If you are logged in and the feature belongs to your private genome, this page will have additional options for you to annotate the feature. These are described [[SEED_Viewer_Manual/Editing_Capabilities/Evidence|here]]. == Visual Protein Evidence == After loading the Evidence Page, the first tab of the [[WebComponent/Tabview|TabView]] is selected. It visually shows different pre-computed tool results for the given feature. In this view, you can see evidence for ''Location'' of the product of the gene in the cell, evidence for protein ''Domains'' and evidence that show ''Similarities'' to other features. === Location === '''Location''' stand for location of the product of the feature in the cell. This section presents output for tools that look for transmembrane helices (TM) or signal peptides (SP) in the feature. In the example, you can see five transmembrane helices in the protein identified via the Phobius tool. They are visualized as little boxes, and their location on the line depicts the location of the transmembrane helices in the protein. [[Image:EvidenceLocation.png]] === Domains === This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the full length of the protein). Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]]''' in the menu bar. [[Image:EvidenceDomain.png]] === Similarities === This section graphically lists evidence for similarities to other features in the SEED and other databases. The '''E-Value Key''' shown on the top defines the colors that are used to display different E-Value ranges for the similarities to the hit features. Hovering over the E-Value Key shows the value range for each color. Each similarity is represented by two bars, showing the alignment of the similarity. The first bar is the '''query''' feature, the second the '''hit''' feature. The abbreviation in front of this bar informs you about the organism the hit feature is in. Hover over the abbreviation to get the complete organism name. To the right of the checkbox you can find the [[Glossary#Functional role|functional role]] of the hit feature. The length of the outside box shows the complete length of the respective sequence. The color of the outside box represents the range of the evalue score according to the E-Value Key bar. The length of the inner (white) box depicts the actual section of the sequence the similarity to the other feature is in. Hovering over the box will show you some information about the hit feature (see tooltip graphics below), including the [[Glossary#Functional role|functional role]], the [[Glossary#Subsystem|subsystems]] and some values describing the hit area. If you check some of the checkboxes in front of the [[Glossary#Functional role|functional role]] descriptions of the hit genes, you can access two functions via the buttons on top of the Similarity graphics. The button '''Align Selected''' leads to an [[SEED_Viewer_Manual/AlignSeqs|alignment page]] showing a TCoffee alignment for the selected features. '''FASTA Download Selected''' lets you download the selected sequences in aminoacid FASTA format. [[Image:EvidenceSims1.png]] [[Image:EvidenceHoverSim.png]] To change the evidence view with respect to the sorting and the filtering of the hits, you can find a little control box on top of the similarity graphics. '''Max Sims''' is the number of similarities that are listed on the page. '''Max E-Value''' filters out all similarities that have a higher E-Value than stated here. In the little combo box below these two values, you can decide to see only hits against the SEED database ('''Just FIG IDs'''), or also against other databases ('''Show all Databases'''). You can '''Sort''' the '''Results By''' ''Score'', ''Percent Identity'' (default) or ''Score per position''. These values locally refer to the hit as known from BLAST hits, so a high percent identity referring to a very small hit region can make this similarity show up as one of the first hits, as shown in the example. Checking '''Group by Genome''' will aggregate all hits to features in the same genome. A blue box will mark hits that belong to the same genome. After selecting the right values, you can press the button '''Resubmit''' to change the evidence view. [[Image:EvidenceFil1.png]] == Tabular Protein Evidence == Activate the second tab of the large page-spanning [[WebComponents/Tabview|TabView]] to see the tabular view of the evidence. You will find most of the information already shown in the visual view, presented differently and enriched with some additional information. Added are the '''Identical Proteins''' and the '''Functionally coupled''' sections, while '''Location''' information is not presented in this tab. === Similarities === The similarity [[WebComponents/Table|table]] lists hits to similar features in the SEED and other databases, as described at [[SEED_Viewer_Manual/Evidence#Visual Protein Evidence|Visual Protein Evidence]]. Each row in the table represents a hit. The first column provides a checkbox to select a hit feature. Again, the buttons '''Align Selected''' and '''FASTA Download Selected''' are present and can be used to get to a TCoffee [[SEED_Viewer_Manual/AlignSeqs|alignment page]] or download the protein sequences of the selected features in FASTA format. The two buttons in the column header allow mass selection of the features. '''All''' will select all features visible in the table, '''check to last checked''' lets you select all features up to a selected feature in the [[WebComponents/Table|table]]. The ID of the hit features, as well as a link to the [[SEED_Viewer_Manual/Annotation|annotation page]] is displayed in the column '''Similar FIG Sequence'''. The next four columns describe information to the hit regions of the query and hit features ('''E-value''', '''Percent Identity''', '''Region in Query peg''' and '''Region in Similar Sequence'''). The '''Organism''' of the hit peg and its '''Function''' are shown in the next two columns. If the function is different from the function of the query feature, it is colored. Same function in the table will get the same color. '''Associated Subsystems'' of the feature are displayed in the next column. If the feature is not associated to a subsystem, you will find the text ''None added'' in the cell. There are three '''Evidence Codes''' that can be found in the last column. ''ISU'' means that the feature is unique in a cell of a subsystem. This means that there is no other feature in the genome that is thought to have the same function. ICW(number) means the feature is clustered with ''number'' features in the genome. ''FF'' says that it is in a [[Glossary#FIGfam|FIGfam]]. The [[WebComponents/Table|table]] can be exported via the button '''export table''' that can be found on top of the table. [[Image:EvidenceSims2.png]] You can filter and sort the table using the [[WebComponents/Tabview|TabView]] above the table. The second tab, '''Sims Filter''' works the same way as described for the Similarities in the [[SEED_Viewer_Manual/Evidence#Visual Protein Evidence|Visual Protein Evidence]]. The first tab '''Edit Columns''' contains a number of columns with additional information that can be added to the display of the table ([[Glossary#FIGfams|FIGfams]], different aliases to other databases and many others). Just choose a column name, press the arrow to put it into the right field and it will add it to the table. [[Image:EvidenceFilter.png]] === Domains === This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the whole length of the protein). The [[WebComponents/Table|table]] lists the '''Domain DB''' (the database for the domain that was hit), the '''ID''' in the domain database, the '''Name''' of the domain, the '''Location''' of the hit in the selected feature, the '''Score''' for the hit against the domain, as well as the '''Function''' of the domain. The table can be exported using the '''export table''' button. Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]]''' in the menu bar. [[Image:EvidenceDomTable.png]] === Identical Proteins === '''Essentially Identical Proteins''' are proteins that share a common sequence, but the start position of the proteins may vary a little. This definition was made because in different databases or close strains of organisms, it often happens that a protein is present, but the start position may be shifted in the finding genes step. So essentially, this table shows aliases of the feature that were based on protein identity. The first column of the [[WebComponents/Table|table]] shows the '''Database''' the alias can be found in, while the second column ('''ID''') offers the alias name and a link to the protein in the respective database. The following two columns describe the '''Organism''' and the '''Assignment''' for the feature for the alias. [[Image:EvidenceEIPs.png]] === Functionally Coupled === This [[WebComponents/Table|table]] lists all [[Glossary#Functional coupling|functionally coupled]] genes in the organism. You can see the '''Score''', the '''ID''' of the feature and the '''Function''' of the feature. [[Image:EvidenceFCs.png]] d2317cc88af662f48d8f9c8504fdd76818c0965b 0 1598 2384 2382 2008-12-05T10:00:55Z DanielaBartels 10 /* Editing Capabilities - Evidence Page */ wikitext text/x-wiki == Editing Capabilities - Evidence Page == If you have the right to edit the feature for which the [[SEED_Viewer_Manual/Evidence|Evidence Page]] is displayed, there will be some additional options visible in the ''[[SEED_Viewer_Manual/Evidence#Tabular Protein Evidence|Tabular Protein Evidence tab]]''. [[Image:EditEvidence1.png]] 4538c25b672f25bfc7782a23de9f8c76b4a7dc3e 2387 2384 2008-12-05T10:08:10Z DanielaBartels 10 /* Editing Capabilities - Evidence Page */ wikitext text/x-wiki == Editing Capabilities - Evidence Page == If you have the right to edit the feature for which the [[SEED_Viewer_Manual/Evidence|Evidence Page]] is displayed, there will be some additional options visible in the ''[[SEED_Viewer_Manual/Evidence#Tabular Protein Evidence|Tabular Protein Evidence tab]]''. The fields to enter a new function are the same as in the [[SEED_Viewer_Manual/Editing_Capabilities/Annotation|Editing capability in the Annotation Page]]. The new function is assigned to all selected features in the table below the fields (use the checkboxes in the first column of the [[WebComponents/Table|table]]). If you have entered a new function, press '''Assign Function''' to annotate the selected features. To assign the selected features with an already existing function from the table, select the feature assigned with the function with the radio box in the rightmost column of the table. [[Image:EditEvidence1.png]] 9d4607a2f6494913e85880c3b8fa15c1182e011a 2388 2387 2008-12-05T10:10:38Z DanielaBartels 10 /* Editing Capabilities - Evidence Page */ wikitext text/x-wiki == Editing Capabilities - Evidence Page == If you have the right to edit the feature for which the [[SEED_Viewer_Manual/Evidence|Evidence Page]] is displayed, there will be some additional options visible in the ''[[SEED_Viewer_Manual/Evidence#Tabular Protein Evidence|Tabular Protein Evidence tab]]''. The fields to enter a new function are the same as in the [[SEED_Viewer_Manual/Editing_Capabilities/Annotation|Editing capability in the Annotation Page]]. The new function is assigned to all selected features in the table below the fields (use the checkboxes in the first column of the [[WebComponents/Table|table]]). If you have entered a new function, press '''Assign Function''' to annotate the selected features. To assign the selected features with an already existing function from the table, select the feature assigned with the function with the radio box in the rightmost column of the table, and leave the text fields above empty. [[Image:EditEvidence1.png]] 2c26dbfd91ea53c07b15b20c461d34056537f0e1 2389 2388 2008-12-05T10:11:07Z DanielaBartels 10 /* Editing Capabilities - Evidence Page */ wikitext text/x-wiki == Editing Capabilities - Evidence Page == If you have the right to edit the feature for which the [[SEED_Viewer_Manual/Evidence|Evidence Page]] is displayed, there will be some additional options visible in the ''[[SEED_Viewer_Manual/Evidence#Tabular Protein Evidence|Tabular Protein Evidence tab]]''. The fields to enter a new function are the same as in the [[SEED_Viewer_Manual/Editing_Capabilities/Annotation|Editing capability in the Annotation Page]]. The new function is assigned to all selected features in the table below the fields (use the checkboxes in the first column of the [[WebComponents/Table|table]]). If you have entered a new function, press '''Assign Function''' to annotate the selected features. To assign the selected features with an already existing function from the table, select the feature assigned with the function with the radio box in the rightmost column of the table, and leave the text fields above empty. Again, use the '''Assign Function''' button to make your annotations. [[Image:EditEvidence1.png]] 01664d84bc311d1dde96ffe101ba84b3d9b82a16 6 1600 2385 2008-12-05T10:01:08Z DanielaBartels 10 wikitext text/x-wiki da39a3ee5e6b4b0d3255bfef95601890afd80709 0 1478 2386 2358 2008-12-05T10:01:10Z TobiasPaczian 17 /* Menu Overview */ wikitext text/x-wiki == Menu Overview == The menu is a small bar below the logo of each page. Most menus have submenus that can be accessed via hovering over the menu. Click the submenu entry you want to go to. If no submenu is present, you can directly click the menu itself. === Navigate Menu === This menu is present on every SeedViewer page. The first entry '''Startpage''' will lead to the SeedViewer [[SEED_Viewer_Manual|HomePage]]. '''Organisms''' will open the [[SEED_Viewer_Manual/OrganismSelect|Organism Select]] page. You will see an overview of all organisms in the SEED and are able to select one to view in detail. '''Subsystems''' will do the same for subsystems. '''Scenarios''' lets you browse [[Glossary#Scenarios|Scenarios]] on the [[SEED_Viewer_Manual/Scenarios|Scenarios Page]]. '''FIGFams''' leads to an entry point for browsing [[SEED_Viewer_Manual/FIGfams|FIGfams]]. You can find more information about FIGfams [[Glossary#FIGfam|here]]. The '''BLAST Search''' links to the [[SEED_Viewer_Manual/BLASTOrganism|BLAST Page]]. You will be able to BLAST a sequence against an organism in the SEED. [[Image:MenuNav.png]] === Help Menu === This menu is also present on all SeedViewer pages. The first link '''What is the SEED''' will lead you to the [[Home_of_the_SEED|SEED Homepage]]. Clicking the second link '''How to use the SEED Viewer''' will get you to this wiki. '''Submitting data to SEED''' lets you browse the [[RAST_Tutorial|RAST Tutorial]]. '''Contact''' enables you to write an email to the SEED team. Clicking '''Register''' is the first step to get a user account. It will lead to the [[SEED_Viewer_Manual/Register|Register]] page. '''I forgot my password''' enables you to [[SEED_Viewer_Manual/RequestNewPassword|Request a new password]]. [[Image:MenuHelp.png]] === Organism Menu === In the context of a selected organism, an organism menu will appear. '''General Information''' will lead to the [[SEED_Viewer_Manual/OrganismPage|Organism Page]] of the selected organism. The '''Feature Table''' will open the [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] and show you the features present in that organism. '''Genome Browser''' leads to the [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] for the selected organism. Clicking '''Scenarios''' shows the [[SEED_Viewer_Manual/Scenarios|Scenarios]] page for your organism. '''Subsystems''' opens a page that lets you select subsystems. '''Export''' enables you to [[SEED_Viewer_Manual/DownloadOrganism|download]] the features of your organism. [[Image:MenuOrganism.png]] === Comparative Tools === This menu is also present whenever an organism is viewed. Different kinds of comparisons of your selected organism to other organisms are available here. '''Function based Comparison''' - The [[SEED_Viewer_Manual/CompareMetabolicReconstruction|Compare Metabolic Reconstruction]] will enable you to see the metabolic reconstruction of your selected organism against that of another one. The '''Sequence based Comparison''' [[SEED_Viewer_Manual/MultiGenomeCompare|Multi Genome Compare]] shows a table and a graphics comparing a selected set of organisms projected against your chosen one (BLAST-based). Use the '''KEGG Metabolic Analysis''' [[SEED_Viewer_Manual/KEGG|to project the metabolic capabilities]] of your organism on KEGG maps. Blasting against your organism is enabled using the '''[[SEED_Viewer_Manual/BLASTOrganism|BLAST Search]]'''. [[Image:CompTools.png]] === Feature Menu === Whenever a feature is defined on a SeedViewer page, you will find the '''Feature''' menu for that feature. The '''Feature Overview''' points to the [[SEED_Viewer_Manual/Annotation|Annotation]] page. It shows general information about the feature, als well as a Compare Regions View that displays the feature in its genomic context and in comparison to homologs in other genomes. '''DNA Sequence''' will open a page with the DNA Sequence of the feature (in FASTA format). '''DNA w/ flanking''' not only prints the DNA sequence of the feature, but also includes a user-defined number of bases upstream and downstream of the feature. '''Protein Sequence''' will show you the protein FASTA sequence (translated from the DNA sequence) of the feature. '''Feature Evidence vs. FIG''' and '''Feature Evidence vs. all DB''' link to the [[SEED_Viewer_Manual/Evidence|Evidence]] page. The difference between the two is that the evidence shown for the feature includes only evidence against features in the SEED or also against other databases (e.g. GenBank, SwissProt, UniProt and many others). The evidence page will also allow you to make this selection or change it there. [[Image:MenuFeature.png]] === Feature Tools === This menu is also present if a feature is defined. It lets the user run a variaty of tools using the feature sequence. These include tools that look for transmembrane helices (e.g. [http://www.cbs.dtu.dk/services/TMHMM/ TMHMM]), signal peptides ([http://www.psort.org/ PSORT], [http://www.cbs.dtu.dk/services/SignalP/ SignalP]), protein domains (e.g. [http://www.ebi.ac.uk/interpro/ InterPro], [http://prodom.prabi.fr/prodom/current/html/home.php ProDom]) and others. [[Image:MenuFeatTools.png]] === FIGfams Menu === On SeedViewer pages that deal with [[Glossary#FIGfam|FIGfams]], you will find an additional FIGfams menu. The '''Home''' link leads to the entry page to [[SEED_Viewer_Manual/FIGfams|FIGfams]]. The '''Release History''' will lead you to a [[SEED_Viewer_Manual/FIGfamsRelease|page]] containing a number of statistics about the current release of the FIGfams. '''Download''' will connect you to the FTP server to enable you to download the FIGfams. [[Image:MenuFIGfam.png]] 2ac0906255c46621f877120ced1c456163baa535 2390 2386 2008-12-05T10:21:38Z TobiasPaczian 17 /* Comparative Tools */ wikitext text/x-wiki == Menu Overview == The menu is a small bar below the logo of each page. Most menus have submenus that can be accessed via hovering over the menu. Click the submenu entry you want to go to. If no submenu is present, you can directly click the menu itself. === Navigate Menu === This menu is present on every SeedViewer page. The first entry '''Startpage''' will lead to the SeedViewer [[SEED_Viewer_Manual|HomePage]]. '''Organisms''' will open the [[SEED_Viewer_Manual/OrganismSelect|Organism Select]] page. You will see an overview of all organisms in the SEED and are able to select one to view in detail. '''Subsystems''' will do the same for subsystems. '''Scenarios''' lets you browse [[Glossary#Scenarios|Scenarios]] on the [[SEED_Viewer_Manual/Scenarios|Scenarios Page]]. '''FIGFams''' leads to an entry point for browsing [[SEED_Viewer_Manual/FIGfams|FIGfams]]. You can find more information about FIGfams [[Glossary#FIGfam|here]]. The '''BLAST Search''' links to the [[SEED_Viewer_Manual/BLASTOrganism|BLAST Page]]. You will be able to BLAST a sequence against an organism in the SEED. [[Image:MenuNav.png]] === Help Menu === This menu is also present on all SeedViewer pages. The first link '''What is the SEED''' will lead you to the [[Home_of_the_SEED|SEED Homepage]]. Clicking the second link '''How to use the SEED Viewer''' will get you to this wiki. '''Submitting data to SEED''' lets you browse the [[RAST_Tutorial|RAST Tutorial]]. '''Contact''' enables you to write an email to the SEED team. Clicking '''Register''' is the first step to get a user account. It will lead to the [[SEED_Viewer_Manual/Register|Register]] page. '''I forgot my password''' enables you to [[SEED_Viewer_Manual/RequestNewPassword|Request a new password]]. [[Image:MenuHelp.png]] === Organism Menu === In the context of a selected organism, an organism menu will appear. '''General Information''' will lead to the [[SEED_Viewer_Manual/OrganismPage|Organism Page]] of the selected organism. The '''Feature Table''' will open the [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] and show you the features present in that organism. '''Genome Browser''' leads to the [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] for the selected organism. Clicking '''Scenarios''' shows the [[SEED_Viewer_Manual/Scenarios|Scenarios]] page for your organism. '''Subsystems''' opens a page that lets you select subsystems. '''Export''' enables you to [[SEED_Viewer_Manual/DownloadOrganism|download]] the features of your organism. [[Image:MenuOrganism.png]] === Comparative Tools === This menu is also present whenever an organism is viewed. Different kinds of comparisons of your selected organism to other organisms are available here. '''Function based Comparison''' - The [[SEED_Viewer_Manual/CompareMetabolicReconstruction|Compare Metabolic Reconstruction]] will enable you to see the metabolic reconstruction of your selected organism against that of another one. The '''Sequence based Comparison''' [[SEED_Viewer_Manual/MultiGenomeCompare|Multi Genome Compare]] shows a table and a graphic comparing a selected set of organisms projected against your chosen one (BLAST-based). Use the '''KEGG Metabolic Analysis''' [[SEED_Viewer_Manual/KEGG|to project the metabolic capabilities]] of your organism on KEGG maps. Blasting against your organism is enabled using the '''[[SEED_Viewer_Manual/BLASTOrganism|BLAST Search]]'''. [[Image:CompTools.png]] === Feature Menu === Whenever a feature is defined on a SeedViewer page, you will find the '''Feature''' menu for that feature. The '''Feature Overview''' points to the [[SEED_Viewer_Manual/Annotation|Annotation]] page. It shows general information about the feature, als well as a Compare Regions View that displays the feature in its genomic context and in comparison to homologs in other genomes. '''DNA Sequence''' will open a page with the DNA Sequence of the feature (in FASTA format). '''DNA w/ flanking''' not only prints the DNA sequence of the feature, but also includes a user-defined number of bases upstream and downstream of the feature. '''Protein Sequence''' will show you the protein FASTA sequence (translated from the DNA sequence) of the feature. '''Feature Evidence vs. FIG''' and '''Feature Evidence vs. all DB''' link to the [[SEED_Viewer_Manual/Evidence|Evidence]] page. The difference between the two is that the evidence shown for the feature includes only evidence against features in the SEED or also against other databases (e.g. GenBank, SwissProt, UniProt and many others). The evidence page will also allow you to make this selection or change it there. [[Image:MenuFeature.png]] === Feature Tools === This menu is also present if a feature is defined. It lets the user run a variaty of tools using the feature sequence. These include tools that look for transmembrane helices (e.g. [http://www.cbs.dtu.dk/services/TMHMM/ TMHMM]), signal peptides ([http://www.psort.org/ PSORT], [http://www.cbs.dtu.dk/services/SignalP/ SignalP]), protein domains (e.g. [http://www.ebi.ac.uk/interpro/ InterPro], [http://prodom.prabi.fr/prodom/current/html/home.php ProDom]) and others. [[Image:MenuFeatTools.png]] === FIGfams Menu === On SeedViewer pages that deal with [[Glossary#FIGfam|FIGfams]], you will find an additional FIGfams menu. The '''Home''' link leads to the entry page to [[SEED_Viewer_Manual/FIGfams|FIGfams]]. The '''Release History''' will lead you to a [[SEED_Viewer_Manual/FIGfamsRelease|page]] containing a number of statistics about the current release of the FIGfams. '''Download''' will connect you to the FTP server to enable you to download the FIGfams. [[Image:MenuFIGfam.png]] 55f3d1dabd3affedf08d9b7737ae3e9450e448b8 2391 2390 2008-12-05T10:22:36Z TobiasPaczian 17 /* Comparative Tools */ wikitext text/x-wiki == Menu Overview == The menu is a small bar below the logo of each page. Most menus have submenus that can be accessed via hovering over the menu. Click the submenu entry you want to go to. If no submenu is present, you can directly click the menu itself. === Navigate Menu === This menu is present on every SeedViewer page. The first entry '''Startpage''' will lead to the SeedViewer [[SEED_Viewer_Manual|HomePage]]. '''Organisms''' will open the [[SEED_Viewer_Manual/OrganismSelect|Organism Select]] page. You will see an overview of all organisms in the SEED and are able to select one to view in detail. '''Subsystems''' will do the same for subsystems. '''Scenarios''' lets you browse [[Glossary#Scenarios|Scenarios]] on the [[SEED_Viewer_Manual/Scenarios|Scenarios Page]]. '''FIGFams''' leads to an entry point for browsing [[SEED_Viewer_Manual/FIGfams|FIGfams]]. You can find more information about FIGfams [[Glossary#FIGfam|here]]. The '''BLAST Search''' links to the [[SEED_Viewer_Manual/BLASTOrganism|BLAST Page]]. You will be able to BLAST a sequence against an organism in the SEED. [[Image:MenuNav.png]] === Help Menu === This menu is also present on all SeedViewer pages. The first link '''What is the SEED''' will lead you to the [[Home_of_the_SEED|SEED Homepage]]. Clicking the second link '''How to use the SEED Viewer''' will get you to this wiki. '''Submitting data to SEED''' lets you browse the [[RAST_Tutorial|RAST Tutorial]]. '''Contact''' enables you to write an email to the SEED team. Clicking '''Register''' is the first step to get a user account. It will lead to the [[SEED_Viewer_Manual/Register|Register]] page. '''I forgot my password''' enables you to [[SEED_Viewer_Manual/RequestNewPassword|Request a new password]]. [[Image:MenuHelp.png]] === Organism Menu === In the context of a selected organism, an organism menu will appear. '''General Information''' will lead to the [[SEED_Viewer_Manual/OrganismPage|Organism Page]] of the selected organism. The '''Feature Table''' will open the [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] and show you the features present in that organism. '''Genome Browser''' leads to the [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] for the selected organism. Clicking '''Scenarios''' shows the [[SEED_Viewer_Manual/Scenarios|Scenarios]] page for your organism. '''Subsystems''' opens a page that lets you select subsystems. '''Export''' enables you to [[SEED_Viewer_Manual/DownloadOrganism|download]] the features of your organism. [[Image:MenuOrganism.png]] === Comparative Tools === This menu is also present whenever an organism is viewed. Different kinds of comparisons of your selected organism to other organisms are available here. '''Function based Comparison''' - The [[SEED_Viewer_Manual/CompareMetabolicReconstruction|Compare Metabolic Reconstruction]] will enable you to see the metabolic reconstruction of your selected organism against that of another one. The '''Sequence based Comparison''' [[SEED_Viewer_Manual/MultiGenomeCompare|Multi Genome Compare]] shows a table and a graphic comparing a selected set of organisms projected against your chosen one (BLAST-based). Use the '''KEGG Metabolic Analysis''' [[SEED_Viewer_Manual/KEGG|to project the metabolic capabilities]] of your organism onto KEGG maps. Blasting against your organism is enabled using the '''[[SEED_Viewer_Manual/BLASTOrganism|BLAST Search]]'''. [[Image:CompTools.png]] === Feature Menu === Whenever a feature is defined on a SeedViewer page, you will find the '''Feature''' menu for that feature. The '''Feature Overview''' points to the [[SEED_Viewer_Manual/Annotation|Annotation]] page. It shows general information about the feature, als well as a Compare Regions View that displays the feature in its genomic context and in comparison to homologs in other genomes. '''DNA Sequence''' will open a page with the DNA Sequence of the feature (in FASTA format). '''DNA w/ flanking''' not only prints the DNA sequence of the feature, but also includes a user-defined number of bases upstream and downstream of the feature. '''Protein Sequence''' will show you the protein FASTA sequence (translated from the DNA sequence) of the feature. '''Feature Evidence vs. FIG''' and '''Feature Evidence vs. all DB''' link to the [[SEED_Viewer_Manual/Evidence|Evidence]] page. The difference between the two is that the evidence shown for the feature includes only evidence against features in the SEED or also against other databases (e.g. GenBank, SwissProt, UniProt and many others). The evidence page will also allow you to make this selection or change it there. [[Image:MenuFeature.png]] === Feature Tools === This menu is also present if a feature is defined. It lets the user run a variaty of tools using the feature sequence. These include tools that look for transmembrane helices (e.g. [http://www.cbs.dtu.dk/services/TMHMM/ TMHMM]), signal peptides ([http://www.psort.org/ PSORT], [http://www.cbs.dtu.dk/services/SignalP/ SignalP]), protein domains (e.g. [http://www.ebi.ac.uk/interpro/ InterPro], [http://prodom.prabi.fr/prodom/current/html/home.php ProDom]) and others. [[Image:MenuFeatTools.png]] === FIGfams Menu === On SeedViewer pages that deal with [[Glossary#FIGfam|FIGfams]], you will find an additional FIGfams menu. The '''Home''' link leads to the entry page to [[SEED_Viewer_Manual/FIGfams|FIGfams]]. The '''Release History''' will lead you to a [[SEED_Viewer_Manual/FIGfamsRelease|page]] containing a number of statistics about the current release of the FIGfams. '''Download''' will connect you to the FTP server to enable you to download the FIGfams. [[Image:MenuFIGfam.png]] 691d572082ca7879bb1e940e4aeee14fd149439c 2392 2391 2008-12-05T10:23:05Z TobiasPaczian 17 /* Comparative Tools */ wikitext text/x-wiki == Menu Overview == The menu is a small bar below the logo of each page. Most menus have submenus that can be accessed via hovering over the menu. Click the submenu entry you want to go to. If no submenu is present, you can directly click the menu itself. === Navigate Menu === This menu is present on every SeedViewer page. The first entry '''Startpage''' will lead to the SeedViewer [[SEED_Viewer_Manual|HomePage]]. '''Organisms''' will open the [[SEED_Viewer_Manual/OrganismSelect|Organism Select]] page. You will see an overview of all organisms in the SEED and are able to select one to view in detail. '''Subsystems''' will do the same for subsystems. '''Scenarios''' lets you browse [[Glossary#Scenarios|Scenarios]] on the [[SEED_Viewer_Manual/Scenarios|Scenarios Page]]. '''FIGFams''' leads to an entry point for browsing [[SEED_Viewer_Manual/FIGfams|FIGfams]]. You can find more information about FIGfams [[Glossary#FIGfam|here]]. The '''BLAST Search''' links to the [[SEED_Viewer_Manual/BLASTOrganism|BLAST Page]]. You will be able to BLAST a sequence against an organism in the SEED. [[Image:MenuNav.png]] === Help Menu === This menu is also present on all SeedViewer pages. The first link '''What is the SEED''' will lead you to the [[Home_of_the_SEED|SEED Homepage]]. Clicking the second link '''How to use the SEED Viewer''' will get you to this wiki. '''Submitting data to SEED''' lets you browse the [[RAST_Tutorial|RAST Tutorial]]. '''Contact''' enables you to write an email to the SEED team. Clicking '''Register''' is the first step to get a user account. It will lead to the [[SEED_Viewer_Manual/Register|Register]] page. '''I forgot my password''' enables you to [[SEED_Viewer_Manual/RequestNewPassword|Request a new password]]. [[Image:MenuHelp.png]] === Organism Menu === In the context of a selected organism, an organism menu will appear. '''General Information''' will lead to the [[SEED_Viewer_Manual/OrganismPage|Organism Page]] of the selected organism. The '''Feature Table''' will open the [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] and show you the features present in that organism. '''Genome Browser''' leads to the [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] for the selected organism. Clicking '''Scenarios''' shows the [[SEED_Viewer_Manual/Scenarios|Scenarios]] page for your organism. '''Subsystems''' opens a page that lets you select subsystems. '''Export''' enables you to [[SEED_Viewer_Manual/DownloadOrganism|download]] the features of your organism. [[Image:MenuOrganism.png]] === Comparative Tools === This menu is also present whenever an organism is viewed. Different kinds of comparisons of your selected organism to other organisms are available here. '''Function based Comparison''' - The [[SEED_Viewer_Manual/CompareMetabolicReconstruction|Compare Metabolic Reconstruction]] will enable you to see the metabolic reconstruction of your selected organism against that of another one. The '''Sequence based Comparison''' [[SEED_Viewer_Manual/MultiGenomeCompare|Multi Genome Compare]] shows a table and a graphic comparing a selected set of organisms projected against your chosen one (BLAST-based). Use the '''KEGG Metabolic Analysis''' [[SEED_Viewer_Manual/KEGG|to project the metabolic capabilities]] of your organism onto KEGG maps. Blasting against your organism is possible using the '''[[SEED_Viewer_Manual/BLASTOrganism|BLAST Search]]'''. [[Image:CompTools.png]] === Feature Menu === Whenever a feature is defined on a SeedViewer page, you will find the '''Feature''' menu for that feature. The '''Feature Overview''' points to the [[SEED_Viewer_Manual/Annotation|Annotation]] page. It shows general information about the feature, als well as a Compare Regions View that displays the feature in its genomic context and in comparison to homologs in other genomes. '''DNA Sequence''' will open a page with the DNA Sequence of the feature (in FASTA format). '''DNA w/ flanking''' not only prints the DNA sequence of the feature, but also includes a user-defined number of bases upstream and downstream of the feature. '''Protein Sequence''' will show you the protein FASTA sequence (translated from the DNA sequence) of the feature. '''Feature Evidence vs. FIG''' and '''Feature Evidence vs. all DB''' link to the [[SEED_Viewer_Manual/Evidence|Evidence]] page. The difference between the two is that the evidence shown for the feature includes only evidence against features in the SEED or also against other databases (e.g. GenBank, SwissProt, UniProt and many others). The evidence page will also allow you to make this selection or change it there. [[Image:MenuFeature.png]] === Feature Tools === This menu is also present if a feature is defined. It lets the user run a variaty of tools using the feature sequence. These include tools that look for transmembrane helices (e.g. [http://www.cbs.dtu.dk/services/TMHMM/ TMHMM]), signal peptides ([http://www.psort.org/ PSORT], [http://www.cbs.dtu.dk/services/SignalP/ SignalP]), protein domains (e.g. [http://www.ebi.ac.uk/interpro/ InterPro], [http://prodom.prabi.fr/prodom/current/html/home.php ProDom]) and others. [[Image:MenuFeatTools.png]] === FIGfams Menu === On SeedViewer pages that deal with [[Glossary#FIGfam|FIGfams]], you will find an additional FIGfams menu. The '''Home''' link leads to the entry page to [[SEED_Viewer_Manual/FIGfams|FIGfams]]. The '''Release History''' will lead you to a [[SEED_Viewer_Manual/FIGfamsRelease|page]] containing a number of statistics about the current release of the FIGfams. '''Download''' will connect you to the FTP server to enable you to download the FIGfams. [[Image:MenuFIGfam.png]] eb4441c47a21161ad7c1054f9c73967fc56a159d 2393 2392 2008-12-05T10:24:45Z TobiasPaczian 17 /* Feature Menu */ wikitext text/x-wiki == Menu Overview == The menu is a small bar below the logo of each page. Most menus have submenus that can be accessed via hovering over the menu. Click the submenu entry you want to go to. If no submenu is present, you can directly click the menu itself. === Navigate Menu === This menu is present on every SeedViewer page. The first entry '''Startpage''' will lead to the SeedViewer [[SEED_Viewer_Manual|HomePage]]. '''Organisms''' will open the [[SEED_Viewer_Manual/OrganismSelect|Organism Select]] page. You will see an overview of all organisms in the SEED and are able to select one to view in detail. '''Subsystems''' will do the same for subsystems. '''Scenarios''' lets you browse [[Glossary#Scenarios|Scenarios]] on the [[SEED_Viewer_Manual/Scenarios|Scenarios Page]]. '''FIGFams''' leads to an entry point for browsing [[SEED_Viewer_Manual/FIGfams|FIGfams]]. You can find more information about FIGfams [[Glossary#FIGfam|here]]. The '''BLAST Search''' links to the [[SEED_Viewer_Manual/BLASTOrganism|BLAST Page]]. You will be able to BLAST a sequence against an organism in the SEED. [[Image:MenuNav.png]] === Help Menu === This menu is also present on all SeedViewer pages. The first link '''What is the SEED''' will lead you to the [[Home_of_the_SEED|SEED Homepage]]. Clicking the second link '''How to use the SEED Viewer''' will get you to this wiki. '''Submitting data to SEED''' lets you browse the [[RAST_Tutorial|RAST Tutorial]]. '''Contact''' enables you to write an email to the SEED team. Clicking '''Register''' is the first step to get a user account. It will lead to the [[SEED_Viewer_Manual/Register|Register]] page. '''I forgot my password''' enables you to [[SEED_Viewer_Manual/RequestNewPassword|Request a new password]]. [[Image:MenuHelp.png]] === Organism Menu === In the context of a selected organism, an organism menu will appear. '''General Information''' will lead to the [[SEED_Viewer_Manual/OrganismPage|Organism Page]] of the selected organism. The '''Feature Table''' will open the [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] and show you the features present in that organism. '''Genome Browser''' leads to the [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] for the selected organism. Clicking '''Scenarios''' shows the [[SEED_Viewer_Manual/Scenarios|Scenarios]] page for your organism. '''Subsystems''' opens a page that lets you select subsystems. '''Export''' enables you to [[SEED_Viewer_Manual/DownloadOrganism|download]] the features of your organism. [[Image:MenuOrganism.png]] === Comparative Tools === This menu is also present whenever an organism is viewed. Different kinds of comparisons of your selected organism to other organisms are available here. '''Function based Comparison''' - The [[SEED_Viewer_Manual/CompareMetabolicReconstruction|Compare Metabolic Reconstruction]] will enable you to see the metabolic reconstruction of your selected organism against that of another one. The '''Sequence based Comparison''' [[SEED_Viewer_Manual/MultiGenomeCompare|Multi Genome Compare]] shows a table and a graphic comparing a selected set of organisms projected against your chosen one (BLAST-based). Use the '''KEGG Metabolic Analysis''' [[SEED_Viewer_Manual/KEGG|to project the metabolic capabilities]] of your organism onto KEGG maps. Blasting against your organism is possible using the '''[[SEED_Viewer_Manual/BLASTOrganism|BLAST Search]]'''. [[Image:CompTools.png]] === Feature Menu === Whenever a feature is defined on a SeedViewer page, you will find the '''Feature''' menu for that feature. The '''Feature Overview''' points to the [[SEED_Viewer_Manual/Annotation|Annotation]] page. It shows general information about the feature, als well as a Compare Regions View that displays the feature in its genomic context and in comparison to homologs in other genomes. '''DNA Sequence''' will open a page with the DNA Sequence of the feature (in FASTA format). '''DNA w/ flanking''' not only prints the DNA sequence of the feature, but also includes a user-defined number of bases upstream and downstream of the feature. '''Protein Sequence''' will show you the protein FASTA sequence (translated from the DNA sequence) of the feature. '''Feature Evidence vs. FIG''' and '''Feature Evidence vs. all DB''' link to the [[SEED_Viewer_Manual/Evidence|Evidence]] page. The difference between the two is that the evidence shown for the feature includes only evidence against features in the SEED or also against other databases (e.g. GenBank, SwissProt, UniProt and many others). The evidence page will also allow you to change this selection. [[Image:MenuFeature.png]] === Feature Tools === This menu is also present if a feature is defined. It lets the user run a variaty of tools using the feature sequence. These include tools that look for transmembrane helices (e.g. [http://www.cbs.dtu.dk/services/TMHMM/ TMHMM]), signal peptides ([http://www.psort.org/ PSORT], [http://www.cbs.dtu.dk/services/SignalP/ SignalP]), protein domains (e.g. [http://www.ebi.ac.uk/interpro/ InterPro], [http://prodom.prabi.fr/prodom/current/html/home.php ProDom]) and others. [[Image:MenuFeatTools.png]] === FIGfams Menu === On SeedViewer pages that deal with [[Glossary#FIGfam|FIGfams]], you will find an additional FIGfams menu. The '''Home''' link leads to the entry page to [[SEED_Viewer_Manual/FIGfams|FIGfams]]. The '''Release History''' will lead you to a [[SEED_Viewer_Manual/FIGfamsRelease|page]] containing a number of statistics about the current release of the FIGfams. '''Download''' will connect you to the FTP server to enable you to download the FIGfams. [[Image:MenuFIGfam.png]] 2b61d7be8b1022acd00a134dd5dea2c25140508a 2394 2393 2008-12-05T10:25:48Z TobiasPaczian 17 /* FIGfams Menu */ wikitext text/x-wiki == Menu Overview == The menu is a small bar below the logo of each page. Most menus have submenus that can be accessed via hovering over the menu. Click the submenu entry you want to go to. If no submenu is present, you can directly click the menu itself. === Navigate Menu === This menu is present on every SeedViewer page. The first entry '''Startpage''' will lead to the SeedViewer [[SEED_Viewer_Manual|HomePage]]. '''Organisms''' will open the [[SEED_Viewer_Manual/OrganismSelect|Organism Select]] page. You will see an overview of all organisms in the SEED and are able to select one to view in detail. '''Subsystems''' will do the same for subsystems. '''Scenarios''' lets you browse [[Glossary#Scenarios|Scenarios]] on the [[SEED_Viewer_Manual/Scenarios|Scenarios Page]]. '''FIGFams''' leads to an entry point for browsing [[SEED_Viewer_Manual/FIGfams|FIGfams]]. You can find more information about FIGfams [[Glossary#FIGfam|here]]. The '''BLAST Search''' links to the [[SEED_Viewer_Manual/BLASTOrganism|BLAST Page]]. You will be able to BLAST a sequence against an organism in the SEED. [[Image:MenuNav.png]] === Help Menu === This menu is also present on all SeedViewer pages. The first link '''What is the SEED''' will lead you to the [[Home_of_the_SEED|SEED Homepage]]. Clicking the second link '''How to use the SEED Viewer''' will get you to this wiki. '''Submitting data to SEED''' lets you browse the [[RAST_Tutorial|RAST Tutorial]]. '''Contact''' enables you to write an email to the SEED team. Clicking '''Register''' is the first step to get a user account. It will lead to the [[SEED_Viewer_Manual/Register|Register]] page. '''I forgot my password''' enables you to [[SEED_Viewer_Manual/RequestNewPassword|Request a new password]]. [[Image:MenuHelp.png]] === Organism Menu === In the context of a selected organism, an organism menu will appear. '''General Information''' will lead to the [[SEED_Viewer_Manual/OrganismPage|Organism Page]] of the selected organism. The '''Feature Table''' will open the [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] and show you the features present in that organism. '''Genome Browser''' leads to the [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] for the selected organism. Clicking '''Scenarios''' shows the [[SEED_Viewer_Manual/Scenarios|Scenarios]] page for your organism. '''Subsystems''' opens a page that lets you select subsystems. '''Export''' enables you to [[SEED_Viewer_Manual/DownloadOrganism|download]] the features of your organism. [[Image:MenuOrganism.png]] === Comparative Tools === This menu is also present whenever an organism is viewed. Different kinds of comparisons of your selected organism to other organisms are available here. '''Function based Comparison''' - The [[SEED_Viewer_Manual/CompareMetabolicReconstruction|Compare Metabolic Reconstruction]] will enable you to see the metabolic reconstruction of your selected organism against that of another one. The '''Sequence based Comparison''' [[SEED_Viewer_Manual/MultiGenomeCompare|Multi Genome Compare]] shows a table and a graphic comparing a selected set of organisms projected against your chosen one (BLAST-based). Use the '''KEGG Metabolic Analysis''' [[SEED_Viewer_Manual/KEGG|to project the metabolic capabilities]] of your organism onto KEGG maps. Blasting against your organism is possible using the '''[[SEED_Viewer_Manual/BLASTOrganism|BLAST Search]]'''. [[Image:CompTools.png]] === Feature Menu === Whenever a feature is defined on a SeedViewer page, you will find the '''Feature''' menu for that feature. The '''Feature Overview''' points to the [[SEED_Viewer_Manual/Annotation|Annotation]] page. It shows general information about the feature, als well as a Compare Regions View that displays the feature in its genomic context and in comparison to homologs in other genomes. '''DNA Sequence''' will open a page with the DNA Sequence of the feature (in FASTA format). '''DNA w/ flanking''' not only prints the DNA sequence of the feature, but also includes a user-defined number of bases upstream and downstream of the feature. '''Protein Sequence''' will show you the protein FASTA sequence (translated from the DNA sequence) of the feature. '''Feature Evidence vs. FIG''' and '''Feature Evidence vs. all DB''' link to the [[SEED_Viewer_Manual/Evidence|Evidence]] page. The difference between the two is that the evidence shown for the feature includes only evidence against features in the SEED or also against other databases (e.g. GenBank, SwissProt, UniProt and many others). The evidence page will also allow you to change this selection. [[Image:MenuFeature.png]] === Feature Tools === This menu is also present if a feature is defined. It lets the user run a variaty of tools using the feature sequence. These include tools that look for transmembrane helices (e.g. [http://www.cbs.dtu.dk/services/TMHMM/ TMHMM]), signal peptides ([http://www.psort.org/ PSORT], [http://www.cbs.dtu.dk/services/SignalP/ SignalP]), protein domains (e.g. [http://www.ebi.ac.uk/interpro/ InterPro], [http://prodom.prabi.fr/prodom/current/html/home.php ProDom]) and others. [[Image:MenuFeatTools.png]] === FIGfams Menu === On SeedViewer pages that deal with [[Glossary#FIGfam|FIGfams]], you will find an additional FIGfams menu. The '''Home''' link leads to the entry page for [[SEED_Viewer_Manual/FIGfams|FIGfams]]. The '''Release History''' will lead you to a [[SEED_Viewer_Manual/FIGfamsRelease|page]] containing a number of statistics about the current release of the FIGfams. '''Download''' will connect you to the FTP server to enable you to download the FIGfams. [[Image:MenuFIGfam.png]] b0b44b2c12e4158b809bed9bf50806df5bc1d472 0 1601 2395 2008-12-05T10:33:51Z DanielaBartels 10 wikitext text/x-wiki == Align Sequences == [[Image:AlignSeqs.png]] 409dfd69325f146c674b873e313ed5ccb1d79e8d 2397 2395 2008-12-05T10:44:59Z DanielaBartels 10 /* Align Sequences */ wikitext text/x-wiki == Align Sequences == [http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html T-Coffee] [[Image:AlignSeqs.png]] a2a6c1868dd7f83a3005937580041baa70b84f4e 2398 2397 2008-12-05T10:49:01Z DanielaBartels 10 /* Align Sequences */ wikitext text/x-wiki == Align Sequences == This page is usually loaded if you have selected a number of features in e.g. the [[SEED_Viewer_Manual/Evidence|Evidence Page]] and pressed an '''Align Sequences''' button. Here, the alignment is presented. The alignment software that is used is [http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html T-Coffee], a method for fast and accurate multiple sequence alignment. On the top of the alignment, you can see a color legend for aligned regions. [[Image:AlignSeqs.png]] 3dec599f727ead38e8b7779abc591645696ae664 2399 2398 2008-12-05T10:49:32Z DanielaBartels 10 /* Align Sequences */ wikitext text/x-wiki == Align Sequences == This page is usually loaded if you have selected a number of features in e.g. the [[SEED_Viewer_Manual/Evidence|Evidence Page]] and pressed an '''Align Sequences''' button. Here, the alignment is presented. The alignment software that is used is [http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html T-Coffee], a method for fast and accurate multiple sequence alignment. On the top of the alignment, you can see a color legend for aligned regions. Below, the multiple alignment for all chosen features is displayed. [[Image:AlignSeqs.png]] f4e098b488d7f3a51dadd9ee48742d4bc04be54e 6 1602 2396 2008-12-05T10:34:08Z DanielaBartels 10 wikitext text/x-wiki da39a3ee5e6b4b0d3255bfef95601890afd80709 0 1517 2400 2360 2008-12-05T10:52:16Z DanielaBartels 10 /* Spreadsheet */ wikitext text/x-wiki == Subsystems == A [[Glossary#Subsystem|subsystem]] is a collection of [[Glossary#Functional role|functional roles]] that are associated to each other in a system. Such a system can for example be a metabolic pathway or a component of a cell like a secretion system. The subsystem page in the SeedViewer is divided into different parts via a [[WebComponents/Tabview|TabView]]. The TabView can consist of 3-5 tabs. The first tab shows a '''Diagram''' of the subsystem, the second tab displays a [[WebComponents/Table|table]] with the '''Functional Roles''' present in the subsystem. The '''Spreadsheet''' relating the functional roles in the subsystem to features in genomes can be found in the third tab. The fourth and fifth tab show a description and additional notes to a subsystem. They only appear if a subsystem has a description / notes. The last tab displays the [[Glossary#Scenarios|Scenarios]] for the subsystem. === Diagram === The subsystem diagram shows the connections between the functional roles in a subsystem. The boxes represent the functional roles via their abbreviations. The circles are connecting intermediates, that are described in the table which is part of the diagram. The functional roles in the diagram can be colored according to their presence in a genome. Click the button '''Color Diagram''' to get a combo box with all genomes in the subsystem. Select your genome of interest and press '''do coloring'''. The boxes for the functional roles defined for that genome will now be colored in green. [[Image:SubsystemDiagram.png]] === Functional Roles === This [[WebComponents/Table|table]] lists all functional roles present in the subsystem. The first column shows '''Group Aliases''' for the functional role. Functional roles can be aggregated in groups (subsets). Subset names that start with a '*' contain alternative ways to implement a function. The abbreviation ('''Abbrev.''') for a functional role must be unique for the functional roles in the subsystem. It is used in different displays like the Diagram or the Speadsheet. The third column lists the full name of the functional role. EC-Numbers are often part of the functional role (for enzymes), and are stated in parentheses after the name of the functional role. The following two columns deal with reactions a functional role is connected to. Clicking on the link opens a new window showing the KEGG reaction. Next to annotator-curated KEGG reactions, we show the KEGG reactions of the curation effort of the [[SEED_People#Hope College|Hope College]] team that collaborates with the SEED. GeneOntology (GO) links are displayed in the next column. The links point to the GO-number in GeneOntology's Amigo-Tool. The last column can contain literature (PubMed IDs) that describes the functional role in detail. If present, you will find a link to PubMed in this column. [[Image:SubsystemFRs.png]] === Spreadsheet === The subsystem spreadsheet displays the features that are assigned with the functional roles in all organisms that are part of the subsystem. The organisms are displayed in the first column. The links lead to the [[SEED_Viewer_Manual/OrganismPage|Organism Page]]. The column header includes a filter option for the organism, doing an infix search on the organism name. The '''Domain''' (Bacterial, Archaeal or Eukaryote) of the organism is shown in the second column. For each organism in the spreadsheet, a '''Variant Code''' is assigned. Usually, there is more than one way to fulfill a subsystem. Metabolic pathways can have alternatives, or parts of the pathway may be present or absent in an organism. [[Glossary#Variant Code|Variant Codes]] are assigned to the organism to express this behavior. There are two special Variant Codes: '''0''' and '''-1'''. The Variant Code '''-1''' means that the organism has no active variant of this subsystem, it is not implement this organism. '''0''' means that the curator has not yet assigned a variant to the genome. Due to the flow of newly sequenced genomes into the SEED, this variant code may show up sometimes. The next column is used to filter active or inactive variants. If you want to see only the active ones (default), enter '''yes''' into the filter in the column header. For seeing only the not active ones, enter '''no'''. No input in this field will show all variants. All following columns in the table show the features in the organisms that are assigned with functional roles. The column headers display the abbreviations of the functional roles (see Functional Roles Table). Hovering over a column header will show a tooltip with the full name of the role. The feature entries in the cells for the functional roles are linked to the [[SEED_Viewer_Manual/Annotation|Annotation Page]] for that feature. There can be multiple features in a cell, as some functions are implemented by more that one feature in an organism. The control table above the spreadsheet table lets you change the display in the table: Functional Roles that belong to a subset starting with a '*', meaning they are alternatives for a function, are collapsed in the spreadsheet by default. If you want to expand the subsets, you can do so by checking '''expanded''' in the '''Subsets''' column. The feature entries in the spreadsheet can be colored according to different metaphors using the second column ('''Coloring''') of the table. By default, the features are colored '''by cluster'''. In this case, it is computed which features are close by on the genomic sequence, meaning they cluster. Each computed cluster gets its own color. These colors only have a meaning per genome, meaning that a yellow cluster in one genome has no connection to a yellow cluster in the next genome. Another way to cluster the features are different kinds of attributes. Check the radio box for '''by attribute''' and choose an attribute in the drop down menu. Press '''update''' to change the display. [[Image:SubsystemSpreadsheet.png]] === Description === The description of a subsystem gives an overview of the functional roles and their connections in the subsystem. It can give some background information about the system, what organisms it is usually found in and other facts that are of interest. === Additional Notes === As the description already gives an overview over the subsystem, additional notes can be found here. The notes usually refer to specific properties of some organisms or organism groups, genes that are missing but should be there and other details that might be useful for the interested user. === Scenarios === The table shows all scenarios that occur in the subsystem. You can see the scenario name, the '''Input Compounds''', the '''Output Compounds''' and a checkbox to decide if you want to see the scenario painted on the [http://www.genome.jp/kegg/ KEGG] map below. If you change the selection of scenarios to paint on the map, click the button '''Paint Map(s)''' to reload the map. You can also select an organism to highlight on the map. Therefore, click the '''Select Organism''' button to get an [[SEED_Viewer_Manual/OrganismSelect]]. After choosing an organism, click the button '''Highlight Reactions for Organism''' to mark the enzymes present in the organism with black boxes. [[Image:SubsystemScenTabs.png]] The [http://www.genome.jp/kegg/ KEGG] map is the first tab of a [[WebComponents/Tabview|TabView]]. The header of the tab includes a link to the map at [http://www.genome.jp/kegg/ KEGG]. Each enzyme in the map is painted with all colors of the scenarios it is part of. A color legend is presented on the right side of the map. The second tab of the [[WebComponents/Tabview|TabView]] shows all reactions that are not shown on the map, but are part of the subsystem. [[Image:SubsystemScenarios.png]] 3befc8945e3c8d06a37e6adf6a00658d18c50ab6 0 1489 2401 1965 2008-12-05T10:58:48Z DanielaBartels 10 /* The Control TabView */ wikitext text/x-wiki == Genome Browser == The Genome Browser enables you to view the features of a genome in their genomic context. The page is divided into three parts, a Control [[WebComponents/Tabview|TabView]], the Six Frame View, and a [[WebComponents/Table|table]] showing all features of an organism. === The Six Frame View === The six frame view represents the six reading frames for proteins (-3, -2, -1, 1, 2, 3). Blue arrows are printed representing protein features. Their direction depicts the strand of the protein (- or +). As RNA features (tRNAs, rRNAs, or other genomic features like binding sites) have no reading frames. They can be found in the middle line of the image, represented by little blue boxes. Hovering over a feature will show a tooltip containing information about the feature, including the name, the position in the genome, the [[Glossary#Functional_role|functional role]] and the [[Glossary#Subsystem|subsystem(s)]] it's in. [[Image:GenomeBrowser6fw.png]] === The Control TabView === Controlling the Six Frame View can be done using the first tab ('''Location''') of the Control TabView. You can choose a location the of the genome you want to view by selecting a contig in the '''contig''' drop down menu and stating a '''start position''' on that contig. The zoom of the window can be changed using the '''window''' drop down box. In addition, features can be colored by different metaphors: by subsystem, by filter options of the Feature Table (the features that are present in the table after filtering it will be colored) or by a user defined list you can specify in the '''Upload List''' tab. Click the button '''Draw''' after making your selections. The arrows '''<=''' and '''=>''' will shift the window over the contig sequence. If you have selected a feature in the Six Frame View, the second tab ('''Focus''') will show you information about the feature (the same information you can find in the tooltip by hovering over the feature). Additionally, you will get three buttons that lead to pages that show more detailed information about the selected feature. The button '''zoom to sequence''' will show you the '''[[SEED_Viewer_Manual/ContigView|DNA to Protein]]''' page depicting a detailed sequence view including the DNA sequence, a six frame view of the translation to protein and other features of the sequence in the area of the selected feature. Clicking '''details page''' leads to the [[SEED_Viewer_Manual/Annotation|Annotation]] page of the feature. You will see all known details about the feature, as well as the [[SEED_Viewer_Manual/Annotation#CompareRegions|Compare regions view]] centered on the feature. The '''evidence''' button leads to the [[SEED_Viewer_Manual/Evidence|Evidence]] page showing evidence for the annotation of the feature in form of Similarities and protein domains. '''Upload a list''' - will let you upload a list of locations of BLAST hits of the form (Contig, Start, Stop, ID). The list has to be in plain text format, meaning not an Excel table. If you have an Excel table containing the information, save the list as '''text (tab delimited)''' in Excel. If you have successfully uploaded a list, you will now be able to navigate the regions in your list. They are shown on the middle line in the Six Frame View in form of little boxes. [[Image:GenomeBrowserLoc.png]] === The Feature Table === The Feature Table shows all features present in your organism in a [[WebComponents/Table|table]]. Information you can see for a feature are its ID, Type (e.g. CDS, RNA and others), its locations (Contig, Start, Stop) and length as well as the functional role it's annotated with and the subsystems it belongs to. The button in the last column (Region) will center the Six Frame View on this feature and select it. [[Image:GenomeBrowserFeat.png]] 1fa22fbf437c42ecf87fd0bc24c9dfdb165daf80 0 1603 2402 2008-12-05T11:03:36Z DanielaBartels 10 wikitext text/x-wiki == Editing Capabilities - Search Gene Page == If you have the right to edit the genome for which the [[SEED_Viewer_Manual/SearchGene|Search Gene Page]] is displayed, you will additional options to '''annotate a found feature''' or '''create a new feature'''. 67d033cc72f91f9fcfb57bef0a8bdcec17a77325 2404 2402 2008-12-05T11:33:11Z DanielaBartels 10 /* Editing Capabilities - Search Gene Page */ wikitext text/x-wiki == Editing Capabilities - Search Gene Page == If you have the right to edit the genome for which the [[SEED_Viewer_Manual/SearchGene|Search Gene Page]] is displayed, you will additional options to '''annotate a found feature''' or '''create a new feature'''. === Annotate a found feature === The BLAST [[WebComponents/Table|table]] now has an additional column on the left to check the hit feature. If you click the newly appeared button '''Assign Role''', you will annotate the hit feature with the function of the matched feature. The arrows in the graphics in the '''Is the gene maybe not called?''' section are linked to the [[SEED_Viewer_Manual/Annotation|Annotation Page]] where you will also have the option to annotate the feature if you have the right to [[SEED_Viewer_Manual/Editing_Capabilities/Annotation|edit the feature]]. === Create new feature === If you have found a missing feature in the tblastn graphics, you can click the hit (marked by a ''Q'') to get to the [[SEED_Viewer_Manual/Editing_Capabilities/CreateFeature|Create Feature]] page. 6c65913b6f1bcf1b0ee641747727655f8d94e55a 0 1493 2403 2364 2008-12-05T11:31:25Z TobiasPaczian 17 /* The Annotation Overview */ wikitext text/x-wiki == Annotation == The Annotation page shows a variaty of information about a single feature like a protein or an RNA. The page is roughly divided into three parts. The '''Annotation Overview''' presents the basic information about the feature. '''Reasons for Current Assignment''' reflect why the feature was assigned with the current functional role. The third part is a '''Compare Regions View''' showing the region of the feature in context to its own and related genomes. If you are logged in and the feature belongs to your private genome, this page will have additional options for you to annotate the feature. These are described [[SEED_Viewer_Manual/Editing_Capabilities/Annotation|here]]. === The Annotation Overview === The feature ID and the genome it belongs to are shown in the header line of this part of the page. They link to [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] and the [[SEED_Viewer_Manual/OrganismPage|Organism Page]], respectively. The '''current annotation''' depicts the functional role that is currently assigned to the feature. As annotations can be changed by our annotators, you have the option to view an annotation history by pressing the '''show''' button in the cell '''annotation history''' some rows below. It will open a small table listing the date, the curator and the annotation that was made for each entry. As the genome name for the feature is already presented in the header of this section, we additionally show the '''taxonomy id''' for that genome in the overview. The link will lead to the Taxonomy Browser at the NCBI showing the taxonomy information for that genome. Behind the taxonomy for the genome you can find the '''contig''' the feature can be found on. The '''internal links''' you can see in the next row are leading to different pages containing other views and information for the feature. The [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] ('''genome browser''') displays the feature in the context of its genome. '''evidence''' leads to the [[SEED_Viewer_Manual/Evidence|Evidence]] page showing evidence for the annotation of the feature in form of Similarities and protein domains. Downloading the actual sequence for the feature is possible using the [[SEED_Viewer_Manual/ShowSeqs|Sequence Page]] ('''sequence''') link. Behind the external links you find a link to the '''ACH''' essentially identical genes. This link leads to the [[AnnotationClearingHouse|Annotation Clearing House]], a collection of proteins from many different sources. Proteins that have essentially the same sequence are grouped. For a given ID, you can see all IDs from different sources that belong to this group. At '''PubMed Links''' you can see the PubMed IDs to papers linked to the NCBI Entrez Database. The PubMed IDs shown are direct literature links attached directly to a feature, so-called '''dlits'''. '''FIGfams''' are protein families based on the subsystems technology. If you find an entry in this fields, the feature is part of the stated FIGfam. The link leads to the [[SEED_Viewer_Manual/FIGfams|FIGfam Viewer]]. '''database cross references''' link the feature to its entries (Aliases) in other databases like UniProt, GenBANK and many others. To gain more information about a feature, you can run different tools (e.g. PSI-BLAST, InterPro and many others) on your feature. Select a tool and press the button '''run tool'''. [[Image:AnnotationFeat.png]] === Reasons for Current Assignment === To gain a clue about what evidence an assignment of a functional role to your feature is based on, the text in '''Reasons for Current Assignment''' summarizes important information supporting the annotation. Additional to the information in the overview table, a list of indirect literature ('''ilits''') is decribed in the text. Those are based on direct literature to similar features that have the same functional role. [[Image:AnnotationAnnot.png]] === Compare Regions === The first line of the '''Compare Regions''' is a graphical display of the region of the feature its genome. All proteins are shown as colored arrows, where the direction depicts the strand of the feature. RNAs and other features are small boxes on the line. If two features overlap, the overlapping will be drawn on an (invisible) second line. The graph is centered on the selected feature (numbered 1), which is always colored red. Below you find the same region for orthologs in other (related) organisms, also colored in red. The colors of the other features (as well as the numbers) also represent ortholog (or sometimes also paralog) features. Whenever there are at least two ortholog or paralog features of a kind, a color (and a number) is assigned to them. '''Display Options''' are divided into two ''Regular'' and ''Advanced''. In the '''Regular''' options, you can change the ''Region Size'' and the ''Number of Regions''. Changing the '''Region Size''' enables to zoom in or out of the region. Changing the '''Number of Regions''' will add or remove genomes to your display. Click '''update graphics''' to change the display. The numbers that you put in for these values will be saved as [[SEED_Viewer_Manual/Preferences|preferences]]. [[Image:AnnotationComp.png]] If you click '''Advanced''' options, you will see the default options that are used for the Compare Regions View. The '''Pinned CDS Selection''' refers to the chosen peg and its orthologs in other genomes. The selection of genomes to show in the graphics can be made by ''Similarity'' or ''PCH pin''. The default is '''Similarity''' and means that the genomes are chosen using the similarity of the selected genes to its orthologs in other genomes. A '''PCH''' means a ''pair of close homologs''. [...] In the cell '''Genome Selection''' you can choose to ''collapse close genomes''. For many organism groups, the SEED database contains a number of strains that do not differ too strongly. They can be removed from the display using this option. The genomes in the display can be sorted by '''Phylogeny''' or '''Phylogenetic distance to input CDS'''. In the first case, the genome of the selected peg may not appear on the first line any more, but the genomes in the display are sorted by the overall phylogeny. The second (default) options will show the selected CDSs region on the first line and the other genomes in order of phylogenetic distance to the peg. The '''Evalue cutoff for selection of pinned CDSs''' depicts the minimum similarity CDSs may have to the selected CDS so that the its region is displayed. Defining if CDSs are orthologs or paralogs to a given CDS and therefore colored as such can be done using the '''Evalue cutoff for coloring CDS sets'''. We have implemented two different '''Coloring algorithms''' for the display. Default is a fast algorithm that might not always be absolutely accurate. You can choose a slower, but exact algorithm for coloring if you are unsure. [[Image:AnnotationAdv.png]] The second tab of the Compare Regions tab view lists all visible features in a table, sorted by the genome they appear in. The entries in the '''ID''' column link to the Annotation page of the feature. Additional to Start, Stop, Strand and Functional Role of the feature, you can see a column ''FC'', an ''SS'', a ''Set'' and a ''CL''. '''FC''' stands for ''[[Glossary#Functional Coupling|Functionally coupled]]'', showing the number of features that are coupled to this feature via clustering genomes or other evidence. The '''SS''' column shows the subsystems the feature is in. '''Set''' is the number that is depicted above a colored feature in the graphic. The '''cluster''' buttons in the last column leads to the [[SEED_Viewer_Manual/HomologClusters|Homolog clusters]] page for that feature. [[Image:AnnotationTabl.png]] 7576fcb09268bdcab07f9c17ba30ff05b1bf6ef4 2406 2403 2008-12-05T13:17:08Z TobiasPaczian 17 /* The Annotation Overview */ wikitext text/x-wiki == Annotation == The Annotation page shows a variaty of information about a single feature like a protein or an RNA. The page is roughly divided into three parts. The '''Annotation Overview''' presents the basic information about the feature. '''Reasons for Current Assignment''' reflect why the feature was assigned with the current functional role. The third part is a '''Compare Regions View''' showing the region of the feature in context to its own and related genomes. If you are logged in and the feature belongs to your private genome, this page will have additional options for you to annotate the feature. These are described [[SEED_Viewer_Manual/Editing_Capabilities/Annotation|here]]. === The Annotation Overview === The feature ID and the genome it belongs to are shown in the header line of this part of the page. They link to [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] and the [[SEED_Viewer_Manual/OrganismPage|Organism Page]], respectively. The '''current annotation''' depicts the functional role that is currently assigned to the feature. As annotations can be changed by our annotators, you have the option to view an annotation history by pressing the '''show''' button in the cell '''annotation history''' some rows below. It will open a small table listing the date, the curator and the annotation that was made for each entry. As the genome name for the feature is already presented in the header of this section, we additionally show the '''taxonomy id''' for that genome in the overview. The link will lead to the Taxonomy Browser at the NCBI showing the taxonomy information for that genome. To the right of the taxonomy id of the genome you will find the '''contig''' the feature can be found on. The '''internal links''' you can see in the next row are leading to different pages containing other views and information for the feature. The [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] ('''genome browser''') displays the feature in the context of its genome. '''evidence''' leads to the [[SEED_Viewer_Manual/Evidence|Evidence]] page showing evidence for the annotation of the feature in form of Similarities and protein domains. Downloading the actual sequence for the feature is possible using the [[SEED_Viewer_Manual/ShowSeqs|Sequence Page]] ('''sequence''') link. Behind the external links you find a link to the '''ACH''' essentially identical genes. This link leads to the [[AnnotationClearingHouse|Annotation Clearing House]], a collection of proteins from many different sources. Proteins that have essentially the same sequence are grouped. For a given ID, you can see all IDs from different sources that belong to this group. At '''PubMed Links''' you can see the PubMed IDs to papers linked to the NCBI Entrez Database. The PubMed IDs shown are direct literature links attached directly to a feature, so-called '''dlits'''. '''FIGfams''' are protein families based on the subsystems technology. If you find an entry in this fields, the feature is part of the stated FIGfam. The link leads to the [[SEED_Viewer_Manual/FIGfams|FIGfam Viewer]]. '''database cross references''' link the feature to its entries (Aliases) in other databases like UniProt, GenBANK and many others. To gain more information about a feature, you can run different tools (e.g. PSI-BLAST, InterPro and many others) on your feature. Select a tool and press the button '''run tool'''. [[Image:AnnotationFeat.png]] === Reasons for Current Assignment === To gain a clue about what evidence an assignment of a functional role to your feature is based on, the text in '''Reasons for Current Assignment''' summarizes important information supporting the annotation. Additional to the information in the overview table, a list of indirect literature ('''ilits''') is decribed in the text. Those are based on direct literature to similar features that have the same functional role. [[Image:AnnotationAnnot.png]] === Compare Regions === The first line of the '''Compare Regions''' is a graphical display of the region of the feature its genome. All proteins are shown as colored arrows, where the direction depicts the strand of the feature. RNAs and other features are small boxes on the line. If two features overlap, the overlapping will be drawn on an (invisible) second line. The graph is centered on the selected feature (numbered 1), which is always colored red. Below you find the same region for orthologs in other (related) organisms, also colored in red. The colors of the other features (as well as the numbers) also represent ortholog (or sometimes also paralog) features. Whenever there are at least two ortholog or paralog features of a kind, a color (and a number) is assigned to them. '''Display Options''' are divided into two ''Regular'' and ''Advanced''. In the '''Regular''' options, you can change the ''Region Size'' and the ''Number of Regions''. Changing the '''Region Size''' enables to zoom in or out of the region. Changing the '''Number of Regions''' will add or remove genomes to your display. Click '''update graphics''' to change the display. The numbers that you put in for these values will be saved as [[SEED_Viewer_Manual/Preferences|preferences]]. [[Image:AnnotationComp.png]] If you click '''Advanced''' options, you will see the default options that are used for the Compare Regions View. The '''Pinned CDS Selection''' refers to the chosen peg and its orthologs in other genomes. The selection of genomes to show in the graphics can be made by ''Similarity'' or ''PCH pin''. The default is '''Similarity''' and means that the genomes are chosen using the similarity of the selected genes to its orthologs in other genomes. A '''PCH''' means a ''pair of close homologs''. [...] In the cell '''Genome Selection''' you can choose to ''collapse close genomes''. For many organism groups, the SEED database contains a number of strains that do not differ too strongly. They can be removed from the display using this option. The genomes in the display can be sorted by '''Phylogeny''' or '''Phylogenetic distance to input CDS'''. In the first case, the genome of the selected peg may not appear on the first line any more, but the genomes in the display are sorted by the overall phylogeny. The second (default) options will show the selected CDSs region on the first line and the other genomes in order of phylogenetic distance to the peg. The '''Evalue cutoff for selection of pinned CDSs''' depicts the minimum similarity CDSs may have to the selected CDS so that the its region is displayed. Defining if CDSs are orthologs or paralogs to a given CDS and therefore colored as such can be done using the '''Evalue cutoff for coloring CDS sets'''. We have implemented two different '''Coloring algorithms''' for the display. Default is a fast algorithm that might not always be absolutely accurate. You can choose a slower, but exact algorithm for coloring if you are unsure. [[Image:AnnotationAdv.png]] The second tab of the Compare Regions tab view lists all visible features in a table, sorted by the genome they appear in. The entries in the '''ID''' column link to the Annotation page of the feature. Additional to Start, Stop, Strand and Functional Role of the feature, you can see a column ''FC'', an ''SS'', a ''Set'' and a ''CL''. '''FC''' stands for ''[[Glossary#Functional Coupling|Functionally coupled]]'', showing the number of features that are coupled to this feature via clustering genomes or other evidence. The '''SS''' column shows the subsystems the feature is in. '''Set''' is the number that is depicted above a colored feature in the graphic. The '''cluster''' buttons in the last column leads to the [[SEED_Viewer_Manual/HomologClusters|Homolog clusters]] page for that feature. [[Image:AnnotationTabl.png]] 523dc629328a72fcade860ef2df15c2c59fc99c5 2407 2406 2008-12-05T13:19:45Z TobiasPaczian 17 /* The Annotation Overview */ wikitext text/x-wiki == Annotation == The Annotation page shows a variaty of information about a single feature like a protein or an RNA. The page is roughly divided into three parts. The '''Annotation Overview''' presents the basic information about the feature. '''Reasons for Current Assignment''' reflect why the feature was assigned with the current functional role. The third part is a '''Compare Regions View''' showing the region of the feature in context to its own and related genomes. If you are logged in and the feature belongs to your private genome, this page will have additional options for you to annotate the feature. These are described [[SEED_Viewer_Manual/Editing_Capabilities/Annotation|here]]. === The Annotation Overview === The feature ID and the genome it belongs to are shown in the header line of this part of the page. They link to [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] and the [[SEED_Viewer_Manual/OrganismPage|Organism Page]], respectively. The '''current annotation''' depicts the functional role that is currently assigned to the feature. As annotations can be changed by our annotators, you have the option to view an annotation history by pressing the '''show''' button in the cell '''annotation history''' some rows below. It will open a small table listing the date, the curator and the annotation that was made for each entry. As the genome name for the feature is already presented in the header of this section, we additionally show the '''taxonomy id''' for that genome in the overview. The link will lead to the Taxonomy Browser at the NCBI showing the taxonomy information for that genome. To the right of the taxonomy id of the genome you will find the '''contig''' the feature can be found on. The '''internal links''' you can see in the next row lead to different pages containing other views and information about the feature. The [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] ('''genome browser''') displays the feature in the context of its genome. '''evidence''' leads to the [[SEED_Viewer_Manual/Evidence|Evidence]] page showing evidence for the annotation of the feature in form of Similarities and protein domains. Downloading the actual sequence for the feature is possible using the [[SEED_Viewer_Manual/ShowSeqs|Sequence Page]] ('''sequence''') link. Behind the external links you find a link to the '''ACH''' essentially identical genes. This link leads to the [[AnnotationClearingHouse|Annotation Clearing House]], a collection of proteins from many different sources. Proteins that have essentially the same sequence are grouped. For a given ID, you can see all IDs from different sources that belong to this group. At '''PubMed Links''' you can see the PubMed IDs of papers linked to the NCBI Entrez Database. The PubMed IDs shown are direct literature links attached directly to a feature, so-called '''dlits'''. '''FIGfams''' are protein families based on the subsystems technology. If you find an entry in this fields, the feature is part of the stated FIGfam. The link leads to the [[SEED_Viewer_Manual/FIGfams|FIGfam Viewer]]. '''database cross references''' link the feature to its entries (Aliases) in other databases like UniProt, GenBANK and many others. To gain more information about a feature, you can run different tools (e.g. PSI-BLAST, InterPro and many others) on your feature. Select a tool and press the button '''run tool'''. [[Image:AnnotationFeat.png]] === Reasons for Current Assignment === To gain a clue about what evidence an assignment of a functional role to your feature is based on, the text in '''Reasons for Current Assignment''' summarizes important information supporting the annotation. Additional to the information in the overview table, a list of indirect literature ('''ilits''') is decribed in the text. Those are based on direct literature to similar features that have the same functional role. [[Image:AnnotationAnnot.png]] === Compare Regions === The first line of the '''Compare Regions''' is a graphical display of the region of the feature its genome. All proteins are shown as colored arrows, where the direction depicts the strand of the feature. RNAs and other features are small boxes on the line. If two features overlap, the overlapping will be drawn on an (invisible) second line. The graph is centered on the selected feature (numbered 1), which is always colored red. Below you find the same region for orthologs in other (related) organisms, also colored in red. The colors of the other features (as well as the numbers) also represent ortholog (or sometimes also paralog) features. Whenever there are at least two ortholog or paralog features of a kind, a color (and a number) is assigned to them. '''Display Options''' are divided into two ''Regular'' and ''Advanced''. In the '''Regular''' options, you can change the ''Region Size'' and the ''Number of Regions''. Changing the '''Region Size''' enables to zoom in or out of the region. Changing the '''Number of Regions''' will add or remove genomes to your display. Click '''update graphics''' to change the display. The numbers that you put in for these values will be saved as [[SEED_Viewer_Manual/Preferences|preferences]]. [[Image:AnnotationComp.png]] If you click '''Advanced''' options, you will see the default options that are used for the Compare Regions View. The '''Pinned CDS Selection''' refers to the chosen peg and its orthologs in other genomes. The selection of genomes to show in the graphics can be made by ''Similarity'' or ''PCH pin''. The default is '''Similarity''' and means that the genomes are chosen using the similarity of the selected genes to its orthologs in other genomes. A '''PCH''' means a ''pair of close homologs''. [...] In the cell '''Genome Selection''' you can choose to ''collapse close genomes''. For many organism groups, the SEED database contains a number of strains that do not differ too strongly. They can be removed from the display using this option. The genomes in the display can be sorted by '''Phylogeny''' or '''Phylogenetic distance to input CDS'''. In the first case, the genome of the selected peg may not appear on the first line any more, but the genomes in the display are sorted by the overall phylogeny. The second (default) options will show the selected CDSs region on the first line and the other genomes in order of phylogenetic distance to the peg. The '''Evalue cutoff for selection of pinned CDSs''' depicts the minimum similarity CDSs may have to the selected CDS so that the its region is displayed. Defining if CDSs are orthologs or paralogs to a given CDS and therefore colored as such can be done using the '''Evalue cutoff for coloring CDS sets'''. We have implemented two different '''Coloring algorithms''' for the display. Default is a fast algorithm that might not always be absolutely accurate. You can choose a slower, but exact algorithm for coloring if you are unsure. [[Image:AnnotationAdv.png]] The second tab of the Compare Regions tab view lists all visible features in a table, sorted by the genome they appear in. The entries in the '''ID''' column link to the Annotation page of the feature. Additional to Start, Stop, Strand and Functional Role of the feature, you can see a column ''FC'', an ''SS'', a ''Set'' and a ''CL''. '''FC''' stands for ''[[Glossary#Functional Coupling|Functionally coupled]]'', showing the number of features that are coupled to this feature via clustering genomes or other evidence. The '''SS''' column shows the subsystems the feature is in. '''Set''' is the number that is depicted above a colored feature in the graphic. The '''cluster''' buttons in the last column leads to the [[SEED_Viewer_Manual/HomologClusters|Homolog clusters]] page for that feature. [[Image:AnnotationTabl.png]] 2e0cc7a648bd257b69f6f31f3fd2b59bde908038 2408 2407 2008-12-05T13:20:53Z TobiasPaczian 17 /* Reasons for Current Assignment */ wikitext text/x-wiki == Annotation == The Annotation page shows a variaty of information about a single feature like a protein or an RNA. The page is roughly divided into three parts. The '''Annotation Overview''' presents the basic information about the feature. '''Reasons for Current Assignment''' reflect why the feature was assigned with the current functional role. The third part is a '''Compare Regions View''' showing the region of the feature in context to its own and related genomes. If you are logged in and the feature belongs to your private genome, this page will have additional options for you to annotate the feature. These are described [[SEED_Viewer_Manual/Editing_Capabilities/Annotation|here]]. === The Annotation Overview === The feature ID and the genome it belongs to are shown in the header line of this part of the page. They link to [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] and the [[SEED_Viewer_Manual/OrganismPage|Organism Page]], respectively. The '''current annotation''' depicts the functional role that is currently assigned to the feature. As annotations can be changed by our annotators, you have the option to view an annotation history by pressing the '''show''' button in the cell '''annotation history''' some rows below. It will open a small table listing the date, the curator and the annotation that was made for each entry. As the genome name for the feature is already presented in the header of this section, we additionally show the '''taxonomy id''' for that genome in the overview. The link will lead to the Taxonomy Browser at the NCBI showing the taxonomy information for that genome. To the right of the taxonomy id of the genome you will find the '''contig''' the feature can be found on. The '''internal links''' you can see in the next row lead to different pages containing other views and information about the feature. The [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] ('''genome browser''') displays the feature in the context of its genome. '''evidence''' leads to the [[SEED_Viewer_Manual/Evidence|Evidence]] page showing evidence for the annotation of the feature in form of Similarities and protein domains. Downloading the actual sequence for the feature is possible using the [[SEED_Viewer_Manual/ShowSeqs|Sequence Page]] ('''sequence''') link. Behind the external links you find a link to the '''ACH''' essentially identical genes. This link leads to the [[AnnotationClearingHouse|Annotation Clearing House]], a collection of proteins from many different sources. Proteins that have essentially the same sequence are grouped. For a given ID, you can see all IDs from different sources that belong to this group. At '''PubMed Links''' you can see the PubMed IDs of papers linked to the NCBI Entrez Database. The PubMed IDs shown are direct literature links attached directly to a feature, so-called '''dlits'''. '''FIGfams''' are protein families based on the subsystems technology. If you find an entry in this fields, the feature is part of the stated FIGfam. The link leads to the [[SEED_Viewer_Manual/FIGfams|FIGfam Viewer]]. '''database cross references''' link the feature to its entries (Aliases) in other databases like UniProt, GenBANK and many others. To gain more information about a feature, you can run different tools (e.g. PSI-BLAST, InterPro and many others) on your feature. Select a tool and press the button '''run tool'''. [[Image:AnnotationFeat.png]] === Reasons for Current Assignment === For information about what evidence an assignment of a functional role to your feature is based on, the text in '''Reasons for Current Assignment''' summarizes important information supporting the annotation. In addition to the information in the overview table, a list of indirect literature ('''ilits''') is decribed in the text. Those are based on direct literature to similar features that have the same functional role. [[Image:AnnotationAnnot.png]] === Compare Regions === The first line of the '''Compare Regions''' is a graphical display of the region of the feature its genome. All proteins are shown as colored arrows, where the direction depicts the strand of the feature. RNAs and other features are small boxes on the line. If two features overlap, the overlapping will be drawn on an (invisible) second line. The graph is centered on the selected feature (numbered 1), which is always colored red. Below you find the same region for orthologs in other (related) organisms, also colored in red. The colors of the other features (as well as the numbers) also represent ortholog (or sometimes also paralog) features. Whenever there are at least two ortholog or paralog features of a kind, a color (and a number) is assigned to them. '''Display Options''' are divided into two ''Regular'' and ''Advanced''. In the '''Regular''' options, you can change the ''Region Size'' and the ''Number of Regions''. Changing the '''Region Size''' enables to zoom in or out of the region. Changing the '''Number of Regions''' will add or remove genomes to your display. Click '''update graphics''' to change the display. The numbers that you put in for these values will be saved as [[SEED_Viewer_Manual/Preferences|preferences]]. [[Image:AnnotationComp.png]] If you click '''Advanced''' options, you will see the default options that are used for the Compare Regions View. The '''Pinned CDS Selection''' refers to the chosen peg and its orthologs in other genomes. The selection of genomes to show in the graphics can be made by ''Similarity'' or ''PCH pin''. The default is '''Similarity''' and means that the genomes are chosen using the similarity of the selected genes to its orthologs in other genomes. A '''PCH''' means a ''pair of close homologs''. [...] In the cell '''Genome Selection''' you can choose to ''collapse close genomes''. For many organism groups, the SEED database contains a number of strains that do not differ too strongly. They can be removed from the display using this option. The genomes in the display can be sorted by '''Phylogeny''' or '''Phylogenetic distance to input CDS'''. In the first case, the genome of the selected peg may not appear on the first line any more, but the genomes in the display are sorted by the overall phylogeny. The second (default) options will show the selected CDSs region on the first line and the other genomes in order of phylogenetic distance to the peg. The '''Evalue cutoff for selection of pinned CDSs''' depicts the minimum similarity CDSs may have to the selected CDS so that the its region is displayed. Defining if CDSs are orthologs or paralogs to a given CDS and therefore colored as such can be done using the '''Evalue cutoff for coloring CDS sets'''. We have implemented two different '''Coloring algorithms''' for the display. Default is a fast algorithm that might not always be absolutely accurate. You can choose a slower, but exact algorithm for coloring if you are unsure. [[Image:AnnotationAdv.png]] The second tab of the Compare Regions tab view lists all visible features in a table, sorted by the genome they appear in. The entries in the '''ID''' column link to the Annotation page of the feature. Additional to Start, Stop, Strand and Functional Role of the feature, you can see a column ''FC'', an ''SS'', a ''Set'' and a ''CL''. '''FC''' stands for ''[[Glossary#Functional Coupling|Functionally coupled]]'', showing the number of features that are coupled to this feature via clustering genomes or other evidence. The '''SS''' column shows the subsystems the feature is in. '''Set''' is the number that is depicted above a colored feature in the graphic. The '''cluster''' buttons in the last column leads to the [[SEED_Viewer_Manual/HomologClusters|Homolog clusters]] page for that feature. [[Image:AnnotationTabl.png]] 2be80b369f96c03544b96f22d0b55c11733de551 2413 2408 2008-12-05T13:25:37Z TobiasPaczian 17 /* Compare Regions */ wikitext text/x-wiki == Annotation == The Annotation page shows a variaty of information about a single feature like a protein or an RNA. The page is roughly divided into three parts. The '''Annotation Overview''' presents the basic information about the feature. '''Reasons for Current Assignment''' reflect why the feature was assigned with the current functional role. The third part is a '''Compare Regions View''' showing the region of the feature in context to its own and related genomes. If you are logged in and the feature belongs to your private genome, this page will have additional options for you to annotate the feature. These are described [[SEED_Viewer_Manual/Editing_Capabilities/Annotation|here]]. === The Annotation Overview === The feature ID and the genome it belongs to are shown in the header line of this part of the page. They link to [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] and the [[SEED_Viewer_Manual/OrganismPage|Organism Page]], respectively. The '''current annotation''' depicts the functional role that is currently assigned to the feature. As annotations can be changed by our annotators, you have the option to view an annotation history by pressing the '''show''' button in the cell '''annotation history''' some rows below. It will open a small table listing the date, the curator and the annotation that was made for each entry. As the genome name for the feature is already presented in the header of this section, we additionally show the '''taxonomy id''' for that genome in the overview. The link will lead to the Taxonomy Browser at the NCBI showing the taxonomy information for that genome. To the right of the taxonomy id of the genome you will find the '''contig''' the feature can be found on. The '''internal links''' you can see in the next row lead to different pages containing other views and information about the feature. The [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] ('''genome browser''') displays the feature in the context of its genome. '''evidence''' leads to the [[SEED_Viewer_Manual/Evidence|Evidence]] page showing evidence for the annotation of the feature in form of Similarities and protein domains. Downloading the actual sequence for the feature is possible using the [[SEED_Viewer_Manual/ShowSeqs|Sequence Page]] ('''sequence''') link. Behind the external links you find a link to the '''ACH''' essentially identical genes. This link leads to the [[AnnotationClearingHouse|Annotation Clearing House]], a collection of proteins from many different sources. Proteins that have essentially the same sequence are grouped. For a given ID, you can see all IDs from different sources that belong to this group. At '''PubMed Links''' you can see the PubMed IDs of papers linked to the NCBI Entrez Database. The PubMed IDs shown are direct literature links attached directly to a feature, so-called '''dlits'''. '''FIGfams''' are protein families based on the subsystems technology. If you find an entry in this fields, the feature is part of the stated FIGfam. The link leads to the [[SEED_Viewer_Manual/FIGfams|FIGfam Viewer]]. '''database cross references''' link the feature to its entries (Aliases) in other databases like UniProt, GenBANK and many others. To gain more information about a feature, you can run different tools (e.g. PSI-BLAST, InterPro and many others) on your feature. Select a tool and press the button '''run tool'''. [[Image:AnnotationFeat.png]] === Reasons for Current Assignment === For information about what evidence an assignment of a functional role to your feature is based on, the text in '''Reasons for Current Assignment''' summarizes important information supporting the annotation. In addition to the information in the overview table, a list of indirect literature ('''ilits''') is decribed in the text. Those are based on direct literature to similar features that have the same functional role. [[Image:AnnotationAnnot.png]] === Compare Regions === The first line of the '''Compare Regions''' is a graphical display of the chromosomal neighborhood of the feature in its genome. All proteins are shown as colored arrows, where the direction depicts the strand of the feature. RNAs and other features are small boxes on the line. Feature overlaps are resolved by drawing the overlapping feature in a new line. The graph is centered on the selected feature (numbered 1), which is always colored red. Below you find the same region for orthologs in other (related) organisms, also colored in red. The colors of the other features (as well as the numbers) also represent ortholog (or sometimes also paralog) features. Whenever there are at least two ortholog or paralog features of a kind, a color (and a number) is assigned to them. '''Display Options''' are divided into two ''Regular'' and ''Advanced''. In the '''Regular''' options, you can change the ''Region Size'' and the ''Number of Regions''. Changing the '''Region Size''' enables to zoom in or out of the region. Changing the '''Number of Regions''' will add or remove genomes to your display. Click '''update graphics''' to change the display. If you are logged in, the numbers that you put in for these values will be saved as [[SEED_Viewer_Manual/Preferences|preferences]]. [[Image:AnnotationComp.png]] If you click '''Advanced''' options, you will see the default options that are used for the Compare Regions View. The '''Pinned CDS Selection''' refers to the chosen feature and its orthologs in other genomes. The selection of genomes to show in the graphics can be made by ''Similarity'' or ''PCH pin''. The default is '''Similarity''' and means that the genomes are chosen using the similarity of the selected genes to its orthologs in other genomes. A '''PCH''' means a ''pair of close homologs''. [...] In the cell '''Genome Selection''' you can choose to ''collapse close genomes''. For many organism groups, the SEED database contains a number of strains that do not differ too strongly. They can be removed from the display using this option. The genomes in the display can be sorted by '''Phylogeny''' or '''Phylogenetic distance to input CDS'''. In the first case, the genome of the selected peg may not appear on the first line any more, but the genomes in the display are sorted by the overall phylogeny. The second (default) options will show the selected CDSs region on the first line and the other genomes in order of phylogenetic distance to the peg. The '''Evalue cutoff for selection of pinned CDSs''' depicts the minimum similarity CDSs may have to the selected CDS so that the its region is displayed. Defining if CDSs are orthologs or paralogs to a given CDS and therefore colored as such can be done using the '''Evalue cutoff for coloring CDS sets'''. We have implemented two different '''Coloring algorithms''' for the display. Default is a fast algorithm that might not always be absolutely accurate. You can choose a slower, but exact algorithm for coloring if you are unsure. [[Image:AnnotationAdv.png]] The second tab of the Compare Regions tab view lists all visible features in a table, sorted by the genome they appear in. The entries in the '''ID''' column link to the Annotation page of the feature. Additional to Start, Stop, Strand and Functional Role of the feature, you can see a column ''FC'', an ''SS'', a ''Set'' and a ''CL''. '''FC''' stands for ''[[Glossary#Functional Coupling|Functionally coupled]]'', showing the number of features that are coupled to this feature via clustering genomes or other evidence. The '''SS''' column shows the subsystems the feature is in. '''Set''' is the number that is depicted above a colored feature in the graphic. The '''cluster''' buttons in the last column leads to the [[SEED_Viewer_Manual/HomologClusters|Homolog clusters]] page for that feature. [[Image:AnnotationTabl.png]] 126f9156d3521f9c40eaee8e54583c0c4b1f2124 2414 2413 2008-12-05T13:28:02Z TobiasPaczian 17 /* Compare Regions */ wikitext text/x-wiki == Annotation == The Annotation page shows a variaty of information about a single feature like a protein or an RNA. The page is roughly divided into three parts. The '''Annotation Overview''' presents the basic information about the feature. '''Reasons for Current Assignment''' reflect why the feature was assigned with the current functional role. The third part is a '''Compare Regions View''' showing the region of the feature in context to its own and related genomes. If you are logged in and the feature belongs to your private genome, this page will have additional options for you to annotate the feature. These are described [[SEED_Viewer_Manual/Editing_Capabilities/Annotation|here]]. === The Annotation Overview === The feature ID and the genome it belongs to are shown in the header line of this part of the page. They link to [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] and the [[SEED_Viewer_Manual/OrganismPage|Organism Page]], respectively. The '''current annotation''' depicts the functional role that is currently assigned to the feature. As annotations can be changed by our annotators, you have the option to view an annotation history by pressing the '''show''' button in the cell '''annotation history''' some rows below. It will open a small table listing the date, the curator and the annotation that was made for each entry. As the genome name for the feature is already presented in the header of this section, we additionally show the '''taxonomy id''' for that genome in the overview. The link will lead to the Taxonomy Browser at the NCBI showing the taxonomy information for that genome. To the right of the taxonomy id of the genome you will find the '''contig''' the feature can be found on. The '''internal links''' you can see in the next row lead to different pages containing other views and information about the feature. The [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] ('''genome browser''') displays the feature in the context of its genome. '''evidence''' leads to the [[SEED_Viewer_Manual/Evidence|Evidence]] page showing evidence for the annotation of the feature in form of Similarities and protein domains. Downloading the actual sequence for the feature is possible using the [[SEED_Viewer_Manual/ShowSeqs|Sequence Page]] ('''sequence''') link. Behind the external links you find a link to the '''ACH''' essentially identical genes. This link leads to the [[AnnotationClearingHouse|Annotation Clearing House]], a collection of proteins from many different sources. Proteins that have essentially the same sequence are grouped. For a given ID, you can see all IDs from different sources that belong to this group. At '''PubMed Links''' you can see the PubMed IDs of papers linked to the NCBI Entrez Database. The PubMed IDs shown are direct literature links attached directly to a feature, so-called '''dlits'''. '''FIGfams''' are protein families based on the subsystems technology. If you find an entry in this fields, the feature is part of the stated FIGfam. The link leads to the [[SEED_Viewer_Manual/FIGfams|FIGfam Viewer]]. '''database cross references''' link the feature to its entries (Aliases) in other databases like UniProt, GenBANK and many others. To gain more information about a feature, you can run different tools (e.g. PSI-BLAST, InterPro and many others) on your feature. Select a tool and press the button '''run tool'''. [[Image:AnnotationFeat.png]] === Reasons for Current Assignment === For information about what evidence an assignment of a functional role to your feature is based on, the text in '''Reasons for Current Assignment''' summarizes important information supporting the annotation. In addition to the information in the overview table, a list of indirect literature ('''ilits''') is decribed in the text. Those are based on direct literature to similar features that have the same functional role. [[Image:AnnotationAnnot.png]] === Compare Regions === The first line of the '''Compare Regions''' is a graphical display of the chromosomal neighborhood of the feature in its genome. All proteins are shown as colored arrows, where the direction depicts the strand of the feature. RNAs and other features are small boxes on the line. Feature overlaps are resolved by drawing the overlapping feature in a new line. The graph is centered on the selected feature (numbered 1), which is always colored red. Below you find the same region for orthologs in other (related) organisms, also colored in red. The colors of the other features (as well as the numbers) also represent ortholog (or sometimes also paralog) features. Whenever there are at least two ortholog or paralog features of a kind, a color (and a number) is assigned to them. '''Display Options''' are divided into two ''Regular'' and ''Advanced''. In the '''Regular''' options, you can change the ''Region Size'' and the ''Number of Regions''. Changing the '''Region Size''' enables to zoom in or out of the region. Changing the '''Number of Regions''' will add or remove genomes to your display. Click '''update graphics''' to change the display. If you are logged in, the numbers that you put in for these values will be saved as [[SEED_Viewer_Manual/Preferences|preferences]]. [[Image:AnnotationComp.png]] If you click '''Advanced''' options, you will see the default options that are used for the Compare Regions View. The '''Pinned CDS Selection''' refers to the chosen feature and its orthologs in other genomes. The selection of genomes to show in the graphics can be made by ''Similarity'' or ''PCH pin''. The default is '''Similarity''' and means that the genomes are chosen using the similarity of the selected genes to its orthologs in other genomes. A '''PCH''' means a [[Glossary#Pair_of_Close_Homologs_.28PCH.29|pair of close homologs]]. In the cell '''Genome Selection''' you can choose to ''collapse close genomes''. For many organism groups, the SEED database contains a number of strains that do not differ too strongly. They can be removed from the display using this option. The genomes in the display can be sorted by '''Phylogeny''' or '''Phylogenetic distance to input CDS'''. In the first case, the genome of the selected peg may not appear on the first line any more, but the genomes in the display are sorted by the overall phylogeny. The second (default) options will show the selected CDSs region on the first line and the other genomes in order of phylogenetic distance to the peg. The '''Evalue cutoff for selection of pinned CDSs''' depicts the minimum similarity CDSs may have to the selected CDS so that the its region is displayed. Defining if CDSs are orthologs or paralogs to a given CDS and therefore colored as such can be done using the '''Evalue cutoff for coloring CDS sets'''. We have implemented two different '''Coloring algorithms''' for the display. Default is a fast algorithm that might not always be absolutely accurate. You can choose a slower, but exact algorithm for coloring if you are unsure. [[Image:AnnotationAdv.png]] The second tab of the Compare Regions tab view lists all visible features in a table, sorted by the genome they appear in. The entries in the '''ID''' column link to the Annotation page of the feature. Additional to Start, Stop, Strand and Functional Role of the feature, you can see a column ''FC'', an ''SS'', a ''Set'' and a ''CL''. '''FC''' stands for ''[[Glossary#Functional Coupling|Functionally coupled]]'', showing the number of features that are coupled to this feature via clustering genomes or other evidence. The '''SS''' column shows the subsystems the feature is in. '''Set''' is the number that is depicted above a colored feature in the graphic. The '''cluster''' buttons in the last column leads to the [[SEED_Viewer_Manual/HomologClusters|Homolog clusters]] page for that feature. [[Image:AnnotationTabl.png]] 1272fc50fa25a3ab47dd9f08fb8d557c4663192e 2415 2414 2008-12-05T13:32:36Z TobiasPaczian 17 /* Compare Regions */ wikitext text/x-wiki == Annotation == The Annotation page shows a variaty of information about a single feature like a protein or an RNA. The page is roughly divided into three parts. The '''Annotation Overview''' presents the basic information about the feature. '''Reasons for Current Assignment''' reflect why the feature was assigned with the current functional role. The third part is a '''Compare Regions View''' showing the region of the feature in context to its own and related genomes. If you are logged in and the feature belongs to your private genome, this page will have additional options for you to annotate the feature. These are described [[SEED_Viewer_Manual/Editing_Capabilities/Annotation|here]]. === The Annotation Overview === The feature ID and the genome it belongs to are shown in the header line of this part of the page. They link to [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] and the [[SEED_Viewer_Manual/OrganismPage|Organism Page]], respectively. The '''current annotation''' depicts the functional role that is currently assigned to the feature. As annotations can be changed by our annotators, you have the option to view an annotation history by pressing the '''show''' button in the cell '''annotation history''' some rows below. It will open a small table listing the date, the curator and the annotation that was made for each entry. As the genome name for the feature is already presented in the header of this section, we additionally show the '''taxonomy id''' for that genome in the overview. The link will lead to the Taxonomy Browser at the NCBI showing the taxonomy information for that genome. To the right of the taxonomy id of the genome you will find the '''contig''' the feature can be found on. The '''internal links''' you can see in the next row lead to different pages containing other views and information about the feature. The [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] ('''genome browser''') displays the feature in the context of its genome. '''evidence''' leads to the [[SEED_Viewer_Manual/Evidence|Evidence]] page showing evidence for the annotation of the feature in form of Similarities and protein domains. Downloading the actual sequence for the feature is possible using the [[SEED_Viewer_Manual/ShowSeqs|Sequence Page]] ('''sequence''') link. Behind the external links you find a link to the '''ACH''' essentially identical genes. This link leads to the [[AnnotationClearingHouse|Annotation Clearing House]], a collection of proteins from many different sources. Proteins that have essentially the same sequence are grouped. For a given ID, you can see all IDs from different sources that belong to this group. At '''PubMed Links''' you can see the PubMed IDs of papers linked to the NCBI Entrez Database. The PubMed IDs shown are direct literature links attached directly to a feature, so-called '''dlits'''. '''FIGfams''' are protein families based on the subsystems technology. If you find an entry in this fields, the feature is part of the stated FIGfam. The link leads to the [[SEED_Viewer_Manual/FIGfams|FIGfam Viewer]]. '''database cross references''' link the feature to its entries (Aliases) in other databases like UniProt, GenBANK and many others. To gain more information about a feature, you can run different tools (e.g. PSI-BLAST, InterPro and many others) on your feature. Select a tool and press the button '''run tool'''. [[Image:AnnotationFeat.png]] === Reasons for Current Assignment === For information about what evidence an assignment of a functional role to your feature is based on, the text in '''Reasons for Current Assignment''' summarizes important information supporting the annotation. In addition to the information in the overview table, a list of indirect literature ('''ilits''') is decribed in the text. Those are based on direct literature to similar features that have the same functional role. [[Image:AnnotationAnnot.png]] === Compare Regions === The first line of the '''Compare Regions''' is a graphical display of the chromosomal neighborhood of the feature in its genome. All proteins are shown as colored arrows, where the direction depicts the strand of the feature. RNAs and other features are small boxes on the line. Feature overlaps are resolved by drawing the overlapping feature in a new line. The graph is centered on the selected feature (numbered 1), which is always colored red. Below you find the same region for orthologs in other (related) organisms, also colored in red. The colors of the other features (as well as the numbers) also represent ortholog (or sometimes also paralog) features. Whenever there are at least two ortholog or paralog features of a kind, a color (and a number) is assigned to them. '''Display Options''' are divided into two ''Regular'' and ''Advanced''. In the '''Regular''' options, you can change the ''Region Size'' and the ''Number of Regions''. Changing the '''Region Size''' enables to zoom in or out of the region. Changing the '''Number of Regions''' will add or remove genomes to your display. Click '''update graphics''' to change the display. If you are logged in, the numbers that you put in for these values will be saved as [[SEED_Viewer_Manual/Preferences|preferences]]. [[Image:AnnotationComp.png]] If you click '''Advanced''' options, you will see the default options that are used for the Compare Regions View. The '''Pinned CDS Selection''' refers to the chosen feature and its orthologs in other genomes. The selection of genomes to show in the graphics can be made by ''Similarity'' or ''PCH pin''. The default is '''Similarity''' and means that the genomes are chosen using the similarity of the selected genes to its orthologs in other genomes. A '''PCH''' stands for [[Glossary#Pair_of_Close_Homologs_.28PCH.29|pair of close homologs]]. In the cell '''Genome Selection''' you can choose to ''collapse close genomes''. For many organism groups, the SEED database contains a number of strains that do not differ too strongly. They can be removed from the display using this option. The genomes in the display can be sorted by '''Phylogeny''' or '''Phylogenetic distance to input CDS'''. In the first case, the genome of the selected feature may not appear on the first line any more, but the genomes in the display are sorted by the overall phylogeny. The second (default) options will show the selected CDSs region on the first line and the other genomes in order of phylogenetic distance to the feature. The '''Evalue cutoff for selection of pinned CDSs''' depicts the minimum similarity CDSs must have to the selected CDS in order for its region to be displayed. Defining if CDSs are orthologs or paralogs to a given CDS and therefore colored as such can be done using the '''Evalue cutoff for coloring CDS sets'''. We have implemented two different '''Coloring algorithms''' for the display. Default is a fast algorithm that might not always be absolutely accurate. You can choose a slower, but exact algorithm for coloring. [[Image:AnnotationAdv.png]] The second tab of the Compare Regions tab view lists all visible features in a table, sorted by the genome they appear in. The entries in the '''ID''' column link to the Annotation page of the feature. In addition to Start, Stop, Strand and Functional Role of the feature, you can see the columns ''FC'', ''SS'', ''Set'' and ''CL''. '''FC''' stands for ''[[Glossary#Functional Coupling|Functionally coupled]]'', showing the number of features that are coupled to this feature via clustering genomes or other evidence. The '''SS''' column shows the subsystems the feature is in. '''Set''' is the number that is depicted above a colored feature in the graphic. The '''cluster''' buttons in the last column lead to the [[SEED_Viewer_Manual/HomologClusters|Homolog clusters]] page for that feature. [[Image:AnnotationTabl.png]] 614dd37235b046a44002e8b240bad810bf4eb8b9 0 1565 2405 2375 2008-12-05T11:34:59Z DanielaBartels 10 /* Editing capabilities in the SeedViewer */ wikitext text/x-wiki == Editing capabilities in the SeedViewer == [[SEED_Viewer_Manual/Editing_Capabilities/Annotation|Annotation Page]] [[SEED_Viewer_Manual/Editing_Capabilities/ChromosomalClusters|Chromosomal Clusters Page]] [[SEED_Viewer_Manual/Editing_Capabilities/Evidence|Evidence Page]] [[SEED_Viewer_Manual/Editing_Capabilities/SearchGene|Search Gene Page]] [[SEED_Viewer_Manual/Editing_Capabilities/CreateFeature|Create new Feature Page]] [[SEED_Viewer_Manual/EditLiterature|Edit Literature for a feature]] c1d458ce42d672c06cfe34093b4d0fccdaf58ac6 0 1604 2409 2008-12-05T13:23:03Z DanielaBartels 10 wikitext text/x-wiki == Editing Capabilities - Create Feature == [[Image:CNFTab.png]] [[Image:CNFActions.png]] [[Image:CreateNewFeature.png]] 7c9b418f406b78e97ea31689294afac94b3fc502 2416 2409 2008-12-05T13:45:13Z DanielaBartels 10 /* Editing Capabilities - Create Feature */ wikitext text/x-wiki == Editing Capabilities - Create Feature == This page lets you create a new protein feature. It consists of three parts, a Control [[WebComponents/Tabview|TabView]], an '''Actions''' panel and the '''Sequence Table'''. === Control TabView === In the first tab of this TabView, you can put in a function for your newly created feature by just entering it into the text field. Below that, you can see two text fields for controlling ''Up/Downstream Nucleotides'''. As you usually enter this page from the [[SEED_Viewer_Manual/SearchGene|Search Gene Page]], you have a hit region defined in which the feature is to be located. The numbers you can enter are the number of upstream and downstream nucleotides of the hit you want to see in the '''Sequence Table'''. The second tab of the TabView lists all codons of the genetic code. Here, you can select the start codons that are possible for the genome you want to create a feature in. Pre-selected are the standard start codons that are usually used for bacterial genomes. You can choose a different set of codons and press the button '''update''' in the '''Actions''' panel to change the view in the '''Sequence Table'''. The genetic code can have small differences from the default genetic code in some organisms. You can change the standard genetic code in the third tab of the TabView. For each triplet, you can see the default amino acid that is usually used in organisms. If you want to change this for a triplet, click the respective drop down box and choose the right amino acid. To make the changes visible in the '''Sequence Table''', press the '''update''' button in the '''Actions''' panel again. [[Image:CNFTab.png]] === Actions panel === [[Image:CNFActions.png]] [[Image:CreateNewFeature.png]] 4ce6010cd8074de5a38681062c9852e52481bb5d 2417 2416 2008-12-05T13:46:03Z DanielaBartels 10 /* Control TabView */ wikitext text/x-wiki == Editing Capabilities - Create Feature == This page lets you create a new protein feature. It consists of three parts, a Control [[WebComponents/Tabview|TabView]], an '''Actions''' panel and the '''Sequence Table'''. === Control TabView === In the first tab of this TabView, you can put in a function for your newly created feature by just entering it into the text field. Below that, you can see two text fields for controlling ''Up/Downstream Nucleotides'''. As you usually enter this page from the [[SEED_Viewer_Manual/SearchGene|Search Gene Page]], you have a hit region defined in which the feature is to be located. The numbers you can enter are the number of upstream and downstream nucleotides of the hit you want to see in the '''Sequence Table'''. After entering your numbers, click the '''update''' button in the '''Actions''' panel The second tab of the TabView lists all codons of the genetic code. Here, you can select the start codons that are possible for the genome you want to create a feature in. Pre-selected are the standard start codons that are usually used for bacterial genomes. You can choose a different set of codons and press the button '''update''' in the '''Actions''' panel to change the view in the '''Sequence Table'''. The genetic code can have small differences from the default genetic code in some organisms. You can change the standard genetic code in the third tab of the TabView. For each triplet, you can see the default amino acid that is usually used in organisms. If you want to change this for a triplet, click the respective drop down box and choose the right amino acid. To make the changes visible in the '''Sequence Table''', press the '''update''' button in the '''Actions''' panel again. [[Image:CNFTab.png]] === Actions panel === [[Image:CNFActions.png]] [[Image:CreateNewFeature.png]] ce1b315b6471229f98510a7e4bfe2d2bbb934213 2418 2417 2008-12-05T15:05:46Z DanielaBartels 10 /* Actions panel */ wikitext text/x-wiki == Editing Capabilities - Create Feature == This page lets you create a new protein feature. It consists of three parts, a Control [[WebComponents/Tabview|TabView]], an '''Actions''' panel and the '''Sequence Table'''. === Control TabView === In the first tab of this TabView, you can put in a function for your newly created feature by just entering it into the text field. Below that, you can see two text fields for controlling ''Up/Downstream Nucleotides'''. As you usually enter this page from the [[SEED_Viewer_Manual/SearchGene|Search Gene Page]], you have a hit region defined in which the feature is to be located. The numbers you can enter are the number of upstream and downstream nucleotides of the hit you want to see in the '''Sequence Table'''. After entering your numbers, click the '''update''' button in the '''Actions''' panel The second tab of the TabView lists all codons of the genetic code. Here, you can select the start codons that are possible for the genome you want to create a feature in. Pre-selected are the standard start codons that are usually used for bacterial genomes. You can choose a different set of codons and press the button '''update''' in the '''Actions''' panel to change the view in the '''Sequence Table'''. The genetic code can have small differences from the default genetic code in some organisms. You can change the standard genetic code in the third tab of the TabView. For each triplet, you can see the default amino acid that is usually used in organisms. If you want to change this for a triplet, click the respective drop down box and choose the right amino acid. To make the changes visible in the '''Sequence Table''', press the '''update''' button in the '''Actions''' panel again. [[Image:CNFTab.png]] === Actions panel === The actions panel consists of three buttons. The '''update''' will let you update the '''Sequence Table''' with new parameters you can type in the '''Control TabView'''. Clicking the second button, '''blastp''' will perform a protein based BLAST of the region selected in the '''Sequence Table'''. For this, you have to choose a ''start'''codon in the table. The sequence taken for the BLAST comparison is the translated protein sequence of the region from that start codon to the next stop codon in that frame. Note that you do not select a '''stop''' codon. If you select a '''stop''' codon, this will be ignored for defining the sequence region. If you have selected a '''start''' codon in the '''Sequence Table''', you can also directly create the feature for that region if you are sure about it. Clicking the '''create''' button will do that. [[Image:CNFActions.png]] [[Image:CreateNewFeature.png]] 9b5f64f6ea63814b1131dea26c895328495a2a82 2419 2418 2008-12-05T15:06:20Z DanielaBartels 10 /* Actions panel */ wikitext text/x-wiki == Editing Capabilities - Create Feature == This page lets you create a new protein feature. It consists of three parts, a Control [[WebComponents/Tabview|TabView]], an '''Actions''' panel and the '''Sequence Table'''. === Control TabView === In the first tab of this TabView, you can put in a function for your newly created feature by just entering it into the text field. Below that, you can see two text fields for controlling ''Up/Downstream Nucleotides'''. As you usually enter this page from the [[SEED_Viewer_Manual/SearchGene|Search Gene Page]], you have a hit region defined in which the feature is to be located. The numbers you can enter are the number of upstream and downstream nucleotides of the hit you want to see in the '''Sequence Table'''. After entering your numbers, click the '''update''' button in the '''Actions''' panel The second tab of the TabView lists all codons of the genetic code. Here, you can select the start codons that are possible for the genome you want to create a feature in. Pre-selected are the standard start codons that are usually used for bacterial genomes. You can choose a different set of codons and press the button '''update''' in the '''Actions''' panel to change the view in the '''Sequence Table'''. The genetic code can have small differences from the default genetic code in some organisms. You can change the standard genetic code in the third tab of the TabView. For each triplet, you can see the default amino acid that is usually used in organisms. If you want to change this for a triplet, click the respective drop down box and choose the right amino acid. To make the changes visible in the '''Sequence Table''', press the '''update''' button in the '''Actions''' panel again. [[Image:CNFTab.png]] === Actions panel === The actions panel consists of three buttons. The '''update''' will let you update the '''Sequence Table''' with new parameters you can type in the '''Control TabView'''. Clicking the second button, '''blastp''' will perform a protein based BLAST of the region selected in the '''Sequence Table'''. For this, you have to choose a '''start'''codon in the table. The sequence taken for the BLAST comparison is the translated protein sequence of the region from that start codon to the next stop codon in that frame. Note that you do not select a '''stop''' codon. If you select a '''stop''' codon, this will be ignored for defining the sequence region. If you have selected a '''start''' codon in the '''Sequence Table''', you can also directly create the feature for that region if you are sure about it. Clicking the '''create''' button will do that. [[Image:CNFActions.png]] [[Image:CreateNewFeature.png]] 1fc0d6b978b0b8361742aa33dcc1b578c5cf56ba 2420 2419 2008-12-05T15:16:43Z DanielaBartels 10 /* Actions panel */ wikitext text/x-wiki == Editing Capabilities - Create Feature == This page lets you create a new protein feature. It consists of three parts, a Control [[WebComponents/Tabview|TabView]], an '''Actions''' panel and the '''Sequence Table'''. === Control TabView === In the first tab of this TabView, you can put in a function for your newly created feature by just entering it into the text field. Below that, you can see two text fields for controlling ''Up/Downstream Nucleotides'''. As you usually enter this page from the [[SEED_Viewer_Manual/SearchGene|Search Gene Page]], you have a hit region defined in which the feature is to be located. The numbers you can enter are the number of upstream and downstream nucleotides of the hit you want to see in the '''Sequence Table'''. After entering your numbers, click the '''update''' button in the '''Actions''' panel The second tab of the TabView lists all codons of the genetic code. Here, you can select the start codons that are possible for the genome you want to create a feature in. Pre-selected are the standard start codons that are usually used for bacterial genomes. You can choose a different set of codons and press the button '''update''' in the '''Actions''' panel to change the view in the '''Sequence Table'''. The genetic code can have small differences from the default genetic code in some organisms. You can change the standard genetic code in the third tab of the TabView. For each triplet, you can see the default amino acid that is usually used in organisms. If you want to change this for a triplet, click the respective drop down box and choose the right amino acid. To make the changes visible in the '''Sequence Table''', press the '''update''' button in the '''Actions''' panel again. [[Image:CNFTab.png]] === Actions panel === The actions panel consists of three buttons. The '''update''' will let you update the '''Sequence Table''' with new parameters you can type in the '''Control TabView'''. Clicking the second button, '''blastp''' will perform a protein based BLAST of the region selected in the '''Sequence Table'''. For this, you have to choose a '''start'''codon in the table. The sequence taken for the BLAST comparison is the translated protein sequence of the region from that start codon to the next stop codon in that frame. Note that you do not select a '''stop''' codon. If you select a '''stop''' codon, this will be ignored for defining the sequence region. If you have selected a '''start''' codon in the '''Sequence Table''', you can also directly create the feature for that region if you are sure about it. Clicking the '''create''' button will do that. [[Image:CNFActions.png]] === Sequence Table === The sequence table is a table of the codons in a genomic region. Each cell represents a triplet. The first line of each line is the translation of that triplet to amino acid. A ''*'' stands for a '''stop''' codon. The second line shows the actual triplet (the codon). The third line can have dots (...), forward arrows (>>>) or reverse arrows (<<<). Dots mean that there not feature overlaps this part of the region. Forward arrows represent a feature on the forward strand, reverse arrows on the reverse strand. This way, you can see if the feature you want to create overlaps with an already present feature in that region. The fourth line sometimes has a check box or a radio box. Radio boxes are shown for every '''start''' codon. Check a radio box to mark the start of the feature. Check boxes are used for '''stop''' codons. Check the check box of a '''stop''' codon to ignore it, meaning that the feature be continue to the next (unchecked) '''stop''' codon. [[Image:CreateNewFeature.png]] 1fc3e033dcc952a18cd598a0baacfb384352a26c 2421 2420 2008-12-05T15:19:25Z DanielaBartels 10 /* Sequence Table */ wikitext text/x-wiki == Editing Capabilities - Create Feature == This page lets you create a new protein feature. It consists of three parts, a Control [[WebComponents/Tabview|TabView]], an '''Actions''' panel and the '''Sequence Table'''. === Control TabView === In the first tab of this TabView, you can put in a function for your newly created feature by just entering it into the text field. Below that, you can see two text fields for controlling ''Up/Downstream Nucleotides'''. As you usually enter this page from the [[SEED_Viewer_Manual/SearchGene|Search Gene Page]], you have a hit region defined in which the feature is to be located. The numbers you can enter are the number of upstream and downstream nucleotides of the hit you want to see in the '''Sequence Table'''. After entering your numbers, click the '''update''' button in the '''Actions''' panel The second tab of the TabView lists all codons of the genetic code. Here, you can select the start codons that are possible for the genome you want to create a feature in. Pre-selected are the standard start codons that are usually used for bacterial genomes. You can choose a different set of codons and press the button '''update''' in the '''Actions''' panel to change the view in the '''Sequence Table'''. The genetic code can have small differences from the default genetic code in some organisms. You can change the standard genetic code in the third tab of the TabView. For each triplet, you can see the default amino acid that is usually used in organisms. If you want to change this for a triplet, click the respective drop down box and choose the right amino acid. To make the changes visible in the '''Sequence Table''', press the '''update''' button in the '''Actions''' panel again. [[Image:CNFTab.png]] === Actions panel === The actions panel consists of three buttons. The '''update''' will let you update the '''Sequence Table''' with new parameters you can type in the '''Control TabView'''. Clicking the second button, '''blastp''' will perform a protein based BLAST of the region selected in the '''Sequence Table'''. For this, you have to choose a '''start'''codon in the table. The sequence taken for the BLAST comparison is the translated protein sequence of the region from that start codon to the next stop codon in that frame. Note that you do not select a '''stop''' codon. If you select a '''stop''' codon, this will be ignored for defining the sequence region. If you have selected a '''start''' codon in the '''Sequence Table''', you can also directly create the feature for that region if you are sure about it. Clicking the '''create''' button will do that. [[Image:CNFActions.png]] === Sequence Table === The sequence table is a table of the codons in a genomic region. Each cell represents a triplet. The first line of each line is the translation of that triplet to amino acid. A ''*'' stands for a '''stop''' codon. The second line shows the actual triplet (the codon). The third line can have dots (...), forward arrows (>>>) or reverse arrows (<<<). Dots mean that there not feature overlaps this part of the region. Forward arrows represent a feature on the forward strand, reverse arrows on the reverse strand. This way, you can see if the feature you want to create overlaps with an already present feature in that region. The fourth line sometimes has a check box or a radio box. Radio boxes are shown for every '''start''' codon. A cell with a start codon is also painted in a green color. Check a radio box to mark the start of the feature. RBS binding sites (purple colored cells) can help to determine the right start codon. Check boxes are used for '''stop''' codons (cells with red color). Check the check box of a '''stop''' codon to ignore it, meaning that the feature be continue to the next (unchecked) '''stop''' codon. [[Image:CreateNewFeature.png]] c3b1a9fb60b802463b457699204d8256634130e4 2422 2421 2008-12-05T16:02:34Z DanielaBartels 10 /* Actions panel */ wikitext text/x-wiki == Editing Capabilities - Create Feature == This page lets you create a new protein feature. It consists of three parts, a Control [[WebComponents/Tabview|TabView]], an '''Actions''' panel and the '''Sequence Table'''. === Control TabView === In the first tab of this TabView, you can put in a function for your newly created feature by just entering it into the text field. Below that, you can see two text fields for controlling ''Up/Downstream Nucleotides'''. As you usually enter this page from the [[SEED_Viewer_Manual/SearchGene|Search Gene Page]], you have a hit region defined in which the feature is to be located. The numbers you can enter are the number of upstream and downstream nucleotides of the hit you want to see in the '''Sequence Table'''. After entering your numbers, click the '''update''' button in the '''Actions''' panel The second tab of the TabView lists all codons of the genetic code. Here, you can select the start codons that are possible for the genome you want to create a feature in. Pre-selected are the standard start codons that are usually used for bacterial genomes. You can choose a different set of codons and press the button '''update''' in the '''Actions''' panel to change the view in the '''Sequence Table'''. The genetic code can have small differences from the default genetic code in some organisms. You can change the standard genetic code in the third tab of the TabView. For each triplet, you can see the default amino acid that is usually used in organisms. If you want to change this for a triplet, click the respective drop down box and choose the right amino acid. To make the changes visible in the '''Sequence Table''', press the '''update''' button in the '''Actions''' panel again. [[Image:CNFTab.png]] === Actions panel === The actions panel consists of three buttons. The '''update''' will let you update the '''Sequence Table''' with new parameters you can type in the '''Control TabView'''. Clicking the second button, '''blastp''' will perform a protein based BLAST of the region selected in the '''Sequence Table'''. For this, you have to choose a '''start'''codon in the table. The sequence taken for the BLAST comparison is the translated protein sequence of the region from that start codon to the next stop codon in that frame. Note that you do not select a '''stop''' codon. If you select a '''stop''' codon, this will be ignored for defining the sequence region. The blast search will result in a [[WebComponents/Table|table]] with all hit proteins. The table shows the hit feature and it's function. You can select a function in this table for the new protein you want to create, instead of putting in a new on in the '''Control TabView''' above. If you have selected a '''start''' codon in the '''Sequence Table''', you can also directly create the feature for that region if you are sure about it. Clicking the '''create''' button will do that. [[Image:CNFActions.png]] === Sequence Table === The sequence table is a table of the codons in a genomic region. Each cell represents a triplet. The first line of each line is the translation of that triplet to amino acid. A ''*'' stands for a '''stop''' codon. The second line shows the actual triplet (the codon). The third line can have dots (...), forward arrows (>>>) or reverse arrows (<<<). Dots mean that there not feature overlaps this part of the region. Forward arrows represent a feature on the forward strand, reverse arrows on the reverse strand. This way, you can see if the feature you want to create overlaps with an already present feature in that region. The fourth line sometimes has a check box or a radio box. Radio boxes are shown for every '''start''' codon. A cell with a start codon is also painted in a green color. Check a radio box to mark the start of the feature. RBS binding sites (purple colored cells) can help to determine the right start codon. Check boxes are used for '''stop''' codons (cells with red color). Check the check box of a '''stop''' codon to ignore it, meaning that the feature be continue to the next (unchecked) '''stop''' codon. [[Image:CreateNewFeature.png]] 950178bddedecfb1d761e115507b8f4908ea52a9 6 1605 2410 2008-12-05T13:23:47Z DanielaBartels 10 wikitext text/x-wiki da39a3ee5e6b4b0d3255bfef95601890afd80709 6 1606 2411 2008-12-05T13:24:04Z DanielaBartels 10 wikitext text/x-wiki da39a3ee5e6b4b0d3255bfef95601890afd80709 6 1607 2412 2008-12-05T13:24:26Z DanielaBartels 10 wikitext text/x-wiki da39a3ee5e6b4b0d3255bfef95601890afd80709 0 1608 2423 2008-12-05T17:01:56Z DanielaBartels 10 wikitext text/x-wiki == Editing Capabilities - Chromosomal Clusters == This page can be accessed from a [[SEED_Viewer_Manual/Annotation#Chromosomal Clusters|Chromosomal Clusters]] view, using the button '''annotate clusters''' (only visible if you have editing rights for the genome). The first table on the page lists all sets of protein visible in the Chromosomal Clusters view. The set numbers in the first column are the set numbers from the view. The second column ('''#features''') shows the number of features in the set. '''#functions''' depicts how many different functions the features in the set have. Whenever there is more than one function, the cell in the next column will be painted in red, as it is not '''consistent''', else green. With the check boxes in the last column, you can turn on and off the details tables for each of the sets. As a default, for each set you will get a details table in the following. These list all the features in the set. The set number is displayed in the first column. '''Organism''' is the genome the feature stems from. If there are more than one occurrence of features in the set for one genome, they are numbered in the '''Occ''' column. If there is a [http://www.uniprot.org UniProt] alias for the feature, the ID and the function of this alias will be shown in the next two columns. 8ba4648da58f9c667f7c8f53d48650de4993d492 2424 2423 2008-12-08T10:43:32Z DanielaBartels 10 /* Editing Capabilities - Chromosomal Clusters */ wikitext text/x-wiki == Editing Capabilities - Chromosomal Clusters == This page can be accessed from a [[SEED_Viewer_Manual/Annotation#Chromosomal Clusters|Chromosomal Clusters]] view, using the button '''annotate clusters''' (only visible if you have editing rights for the genome). The first table on the page lists all sets of protein visible in the Chromosomal Clusters view. The set numbers in the first column are the set numbers from the view. The second column ('''#features''') shows the number of features in the set. '''#functions''' depicts how many different functions the features in the set have. Whenever there is more than one function, the cell in the next column will be painted in red, as it is not '''consistent''', else green. With the check boxes in the last column, you can turn on and off the details tables for each of the sets. [[Image:Chromosomal1.png]] As a default, for each set you will get a details table in the following. These list all the features in the set. The set number is displayed in the first column. '''Organism''' is the genome the feature stems from. If there are more than one occurrence of features in the set for one genome, they are numbered in the '''Occ''' column. If there is a [http://www.uniprot.org UniProt] alias for the feature, the ID and the function of this alias will be shown in the next two columns. 0cc437199a3fe216a6eaf1d35e3c5c1e5594721d 2426 2424 2008-12-08T10:48:48Z DanielaBartels 10 /* Editing Capabilities - Chromosomal Clusters */ wikitext text/x-wiki == Editing Capabilities - Chromosomal Clusters == This page can be accessed from a [[SEED_Viewer_Manual/Annotation#Chromosomal Clusters|Chromosomal Clusters]] view, using the button '''annotate clusters''' (only visible if you have editing rights for the genome). The first table on the page lists all sets of protein visible in the Chromosomal Clusters view. The set numbers in the first column are the set numbers from the view. The second column ('''#features''') shows the number of features in the set. '''#functions''' depicts how many different functions the features in the set have. One of the functions is displayed in the column '''first function'''. Whenever there is more than one function, the cell in the next column will be painted in red, as it is not '''consistent''', else green. With the check boxes in the last column, you can turn on and off the details tables for each of the sets. [[Image:Chromosomal1.png]] As a default, for each set you will get a details table in the following. These list all the features in the set. The set number is displayed in the first column. '''Organism''' is the genome the feature stems from. If there are more than one occurrence of features in the set for one genome, they are numbered in the '''Occ''' column. If there is a [http://www.uniprot.org UniProt] alias for the feature, the ID and the function of this alias will be shown in the next two columns. f5bd17ff209c4a310bc35d42a392a35b8d108cae 2427 2426 2008-12-08T10:56:07Z DanielaBartels 10 /* Editing Capabilities - Chromosomal Clusters */ wikitext text/x-wiki == Editing Capabilities - Chromosomal Clusters == This page can be accessed from a [[SEED_Viewer_Manual/Annotation#Chromosomal Clusters|Chromosomal Clusters]] view, using the button '''annotate clusters''' (only visible if you have editing rights for the genome). === Overview Table === The first table on the page lists all sets of protein visible in the Chromosomal Clusters view. The set numbers in the first column are the set numbers from the view. The second column ('''#features''') shows the number of features in the set. '''#functions''' depicts how many different functions the features in the set have. One of the functions is displayed in the column '''first function'''. Whenever there is more than one function, the cell in the next column will be painted in red, as it is not '''consistent''', else green. With the check boxes in the last column, you can turn on and off the details tables for each of the sets. Above the table, there are four buttons to turn on/off the details tables. '''show all''' will remove previous filtering and show you all details tables again. '''show none''' will remove all details tables, so that you can afterwards select single ones you'd like to see. '''show consistenct''' and '''show inconsistent''' is related to the '''consistent''' column in the table. It will display the details tables with a consistent or an inconsistent set, respectively. [[Image:Chromosomal1.png]] As a default, for each set you will get a details table in the following. These list all the features in the set. The set number is displayed in the first column. '''Organism''' is the genome the feature stems from. If there are more than one occurrence of features in the set for one genome, they are numbered in the '''Occ''' column. If there is a [http://www.uniprot.org UniProt] alias for the feature, the ID and the function of this alias will be shown in the next two columns. 383c9f7373530ff5c4c754de356d8f1405df3f6b 2428 2427 2008-12-08T11:11:45Z DanielaBartels 10 /* Overview Table */ wikitext text/x-wiki == Editing Capabilities - Chromosomal Clusters == This page can be accessed from a [[SEED_Viewer_Manual/Annotation#Chromosomal Clusters|Chromosomal Clusters]] view, using the button '''annotate clusters''' (only visible if you have editing rights for the genome). === Overview Table === The first table on the page lists all sets of protein visible in the Chromosomal Clusters view. The set numbers in the first column are the set numbers from the view. The second column ('''#features''') shows the number of features in the set. '''#functions''' depicts how many different functions the features in the set have. One of the functions is displayed in the column '''first function'''. Whenever there is more than one function, the cell in the next column will be painted in red, as it is not '''consistent''', else green. With the check boxes in the last column, you can turn on and off the details tables for each of the sets. Above the table, there are four buttons to turn on/off the details tables. '''show all''' will remove previous filtering and show you all details tables again. '''show none''' will remove all details tables, so that you can afterwards select single ones you'd like to see. '''show consistenct''' and '''show inconsistent''' is related to the '''consistent''' column in the table. It will display the details tables with a consistent or an inconsistent set, respectively. [[Image:Chromosomal1.png]] === Details table === As a default, for each set you will get a details table in the following. These list all the features in the set. The set number is displayed in the first column. '''Organism''' is the genome the feature stems from. If there are more than one occurrence of features in the set for one genome, they are numbered in the '''Occ''' column. If there is a [http://www.uniprot.org UniProt] alias for the feature, the ID and the function of this alias will be shown in the next two columns. The IDs of the features in the next column '''Feature''' link to the [[SEED_Viewer_Manual/Annotation|Annotation Page]] for that feature. [[Image:Chromosomal2.png]] cd828f639464d552649dbaab4fc63bdf77ea273b 2431 2428 2008-12-08T11:56:01Z DanielaBartels 10 /* Details table */ wikitext text/x-wiki == Editing Capabilities - Chromosomal Clusters == This page can be accessed from a [[SEED_Viewer_Manual/Annotation#Chromosomal Clusters|Chromosomal Clusters]] view, using the button '''annotate clusters''' (only visible if you have editing rights for the genome). === Overview Table === The first table on the page lists all sets of protein visible in the Chromosomal Clusters view. The set numbers in the first column are the set numbers from the view. The second column ('''#features''') shows the number of features in the set. '''#functions''' depicts how many different functions the features in the set have. One of the functions is displayed in the column '''first function'''. Whenever there is more than one function, the cell in the next column will be painted in red, as it is not '''consistent''', else green. With the check boxes in the last column, you can turn on and off the details tables for each of the sets. Above the table, there are four buttons to turn on/off the details tables. '''show all''' will remove previous filtering and show you all details tables again. '''show none''' will remove all details tables, so that you can afterwards select single ones you'd like to see. '''show consistenct''' and '''show inconsistent''' is related to the '''consistent''' column in the table. It will display the details tables with a consistent or an inconsistent set, respectively. [[Image:Chromosomal1.png]] === Details table === As a default, for each set you will get a details table in the following. These list all the features in the set. The set number is displayed in the first column. '''Organism''' is the genome the feature stems from. If there are more than one occurrence of features in the set for one genome, they are numbered in the '''Occ''' column. If there is a [http://www.uniprot.org UniProt] alias for the feature, the ID and the function of this alias will be shown in the next two columns. The IDs of the features in the next column '''Feature''' link to the [[SEED_Viewer_Manual/Annotation|Annotation Page]] for that feature. If the feature is in a subsystem, you will find one or many (comma-separated) numbers in the '''SS''' column. Hovering over the cell will display a tooltip with the names of the subsystems. The column '''Ev''' shows Evidence Codes for the feature. There are three '''Evidence Codes''' that can be found in the last column. ''ISU'' means that the feature is unique in a cell of a subsystem. This means that there is no other feature in the genome that is thought to have the same function. ICW(number) means the feature is clustered with ''number'' features in the genome. ''FF'' says that it is in a [[Glossary#FIGfam|FIGfam]]. The length of the feature is shown in the next column ('''Ln'''). Its current function can be found in the column '''Function'''. Same colors in this column indicate same functions. Links to a [[SEED_Viewer_Manual/FIGfamViewer|FIGfam]] a feature is member of are displayed in the last column. [[Image:Chromosomal2.png]] a7bc0792b92573119cee21808b316d5f7cc02d81 2432 2431 2008-12-08T12:01:15Z DanielaBartels 10 /* Details table */ wikitext text/x-wiki == Editing Capabilities - Chromosomal Clusters == This page can be accessed from a [[SEED_Viewer_Manual/Annotation#Chromosomal Clusters|Chromosomal Clusters]] view, using the button '''annotate clusters''' (only visible if you have editing rights for the genome). === Overview Table === The first table on the page lists all sets of protein visible in the Chromosomal Clusters view. The set numbers in the first column are the set numbers from the view. The second column ('''#features''') shows the number of features in the set. '''#functions''' depicts how many different functions the features in the set have. One of the functions is displayed in the column '''first function'''. Whenever there is more than one function, the cell in the next column will be painted in red, as it is not '''consistent''', else green. With the check boxes in the last column, you can turn on and off the details tables for each of the sets. Above the table, there are four buttons to turn on/off the details tables. '''show all''' will remove previous filtering and show you all details tables again. '''show none''' will remove all details tables, so that you can afterwards select single ones you'd like to see. '''show consistenct''' and '''show inconsistent''' is related to the '''consistent''' column in the table. It will display the details tables with a consistent or an inconsistent set, respectively. [[Image:Chromosomal1.png]] === Details table === As a default, for each set you will get a details table in the following. These list all the features in the set. The set number is displayed in the first column. '''Organism''' is the genome the feature stems from. If there are more than one occurrence of features in the set for one genome, they are numbered in the '''Occ''' column. If there is a [http://www.uniprot.org UniProt] alias for the feature, the ID and the function of this alias will be shown in the next two columns. The IDs of the features in the next column '''Feature''' link to the [[SEED_Viewer_Manual/Annotation|Annotation Page]] for that feature. If the feature is in a subsystem, you will find one or many (comma-separated) numbers in the '''SS''' column. Hovering over the cell will display a tooltip with the names of the subsystems. The column '''Ev''' shows Evidence Codes for the feature. There are three '''Evidence Codes''' that can be found in the last column. ''ISU'' means that the feature is unique in a cell of a subsystem. This means that there is no other feature in the genome that is thought to have the same function. ICW(number) means the feature is clustered with ''number'' features in the genome. ''FF'' says that it is in a [[Glossary#FIGfam|FIGfam]]. The length of the feature is shown in the next column ('''Ln'''). Its current function can be found in the column '''Function'''. Same colors in this column indicate same functions. Links to a [[SEED_Viewer_Manual/FIGfamViewer|FIGfam]] a feature is member of are displayed in the last column. Editing the function for the features in the Details table is done by checking a function or entering a new one, then clicking the '''annotate''' button. You can select a UniProt function, or one of the other feature's functions. If you want to use a new one, enter it in the '''new function''' text field and check the radio box next to it. The new function will be used to annotate all features that are checked in the '''Feature''' column. You will only be able to check features you can edit. In this example, only the ''Escherichia coli K12'' can be edited, so you will find a checkbox only for this feature. [[Image:Chromosomal2.png]] 89eb80bfe48cd289ba3dbf8a190c8a4e05421ce7 2433 2432 2008-12-08T13:26:23Z DanielaBartels 10 /* Details table */ wikitext text/x-wiki == Editing Capabilities - Chromosomal Clusters == This page can be accessed from a [[SEED_Viewer_Manual/Annotation#Chromosomal Clusters|Chromosomal Clusters]] view, using the button '''annotate clusters''' (only visible if you have editing rights for the genome). === Overview Table === The first table on the page lists all sets of protein visible in the Chromosomal Clusters view. The set numbers in the first column are the set numbers from the view. The second column ('''#features''') shows the number of features in the set. '''#functions''' depicts how many different functions the features in the set have. One of the functions is displayed in the column '''first function'''. Whenever there is more than one function, the cell in the next column will be painted in red, as it is not '''consistent''', else green. With the check boxes in the last column, you can turn on and off the details tables for each of the sets. Above the table, there are four buttons to turn on/off the details tables. '''show all''' will remove previous filtering and show you all details tables again. '''show none''' will remove all details tables, so that you can afterwards select single ones you'd like to see. '''show consistenct''' and '''show inconsistent''' is related to the '''consistent''' column in the table. It will display the details tables with a consistent or an inconsistent set, respectively. [[Image:Chromosomal1.png]] === Details table === As a default, for each set you will get a details table in the following. These list all the features in the set. The set number is displayed in the first column. '''Organism''' is the genome the feature stems from. If there are more than one occurrence of features in the set for one genome, they are numbered in the '''Occ''' column. If there is a [http://www.uniprot.org UniProt] alias for the feature, the ID and the function of this alias will be shown in the next two columns. The IDs of the features in the next column '''Feature''' link to the [[SEED_Viewer_Manual/Annotation|Annotation Page]] for that feature. If the feature is in a subsystem, you will find one or many (comma-separated) numbers in the '''SS''' column. Hovering over the cell will display a tooltip with the names of the subsystems. The column '''Ev''' shows Evidence Codes for the feature. There are three '''Evidence Codes''' that can be found in the last column. ''ISU'' means that the feature is unique in a cell of a subsystem. This means that there is no other feature in the genome that is thought to have the same function. ICW(number) means the feature is clustered with ''number'' features in the genome. ''FF'' says that it is in a [[Glossary#FIGfam|FIGfam]]. The length of the feature is shown in the next column ('''Ln'''). Its current function can be found in the column '''Function'''. Same colors in this column indicate same functions. Links to a [[SEED_Viewer_Manual/FIGfamViewer|FIGfam]] a feature is member of are displayed in the last column. Editing the function for the features in the Details table is done by checking a function or entering a new one, then clicking the '''annotate''' button. You can select a UniProt function, or one of the other feature's functions. If you want to use a new one, enter it in the '''new function''' text field and check the radio box next to it. The new function will be used to annotate all features that are checked in the '''Feature''' column. You will only be able to check features you can edit. In this example, only the ''Escherichia coli K12'' can be edited, so you will find a checkbox only for this feature. To align features in the [[SEED_Viewer_Manual/AlignSeqs|Alignment Page]], check the features of interest and press the button '''align'''. The buttons '''check all''', '''uncheck all''' and '''check to last checked''' can be used for the check boxes of the features, which is especially important for large tables. [[Image:Chromosomal2.png]] bc3260999803e13f471ac647b3d2384d85c552ae 6 1609 2425 2008-12-08T10:43:53Z DanielaBartels 10 wikitext text/x-wiki da39a3ee5e6b4b0d3255bfef95601890afd80709 6 1610 2429 2008-12-08T11:12:08Z DanielaBartels 10 wikitext text/x-wiki da39a3ee5e6b4b0d3255bfef95601890afd80709 0 1502 2430 2379 2008-12-08T11:51:33Z DanielaBartels 10 /* Visual Protein Evidence */ wikitext text/x-wiki The Evidence Page is divided into two parts via a [[WebComponents/Tabview|TabView]]: The '''Visual Protein Evidence''' and the '''Tabular Protein Evidence'''. If you are logged in and the feature belongs to your private genome, this page will have additional options for you to annotate the feature. These are described [[SEED_Viewer_Manual/Editing_Capabilities/Evidence|here]]. == Visual Protein Evidence == After loading the Evidence Page, the first tab of the [[WebComponents/Tabview|TabView]] is selected. It visually shows different pre-computed tool results for the given feature. In this view, you can see evidence for ''Location'' of the product of the gene in the cell, evidence for protein ''Domains'' and evidence that show ''Similarities'' to other features. === Location === '''Location''' stand for location of the product of the feature in the cell. This section presents output for tools that look for transmembrane helices (TM) or signal peptides (SP) in the feature. In the example, you can see five transmembrane helices in the protein identified via the Phobius tool. They are visualized as little boxes, and their location on the line depicts the location of the transmembrane helices in the protein. [[Image:EvidenceLocation.png]] === Domains === This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the full length of the protein). Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]]''' in the menu bar. [[Image:EvidenceDomain.png]] === Similarities === This section graphically lists evidence for similarities to other features in the SEED and other databases. The '''E-Value Key''' shown on the top defines the colors that are used to display different E-Value ranges for the similarities to the hit features. Hovering over the E-Value Key shows the value range for each color. Each similarity is represented by two bars, showing the alignment of the similarity. The first bar is the '''query''' feature, the second the '''hit''' feature. The abbreviation in front of this bar informs you about the organism the hit feature is in. Hover over the abbreviation to get the complete organism name. To the right of the checkbox you can find the [[Glossary#Functional role|functional role]] of the hit feature. The length of the outside box shows the complete length of the respective sequence. The color of the outside box represents the range of the evalue score according to the E-Value Key bar. The length of the inner (white) box depicts the actual section of the sequence the similarity to the other feature is in. Hovering over the box will show you some information about the hit feature (see tooltip graphics below), including the [[Glossary#Functional role|functional role]], the [[Glossary#Subsystem|subsystems]] and some values describing the hit area. If you check some of the checkboxes in front of the [[Glossary#Functional role|functional role]] descriptions of the hit genes, you can access two functions via the buttons on top of the Similarity graphics. The button '''Align Selected''' leads to an [[SEED_Viewer_Manual/AlignSeqs|alignment page]] showing a TCoffee alignment for the selected features. '''FASTA Download Selected''' lets you download the selected sequences in aminoacid FASTA format. [[Image:EvidenceSims1.png]] [[Image:EvidenceHoverSim.png]] To change the evidence view with respect to the sorting and the filtering of the hits, you can find a little control box on top of the similarity graphics. '''Max Sims''' is the number of similarities that are listed on the page. '''Max E-Value''' filters out all similarities that have a higher E-Value than stated here. In the little combo box below these two values, you can decide to see only hits against the SEED database ('''Just FIG IDs'''), or also against other databases ('''Show all Databases'''). You can '''Sort''' the '''Results By''' ''Score'', ''Percent Identity'' (default) or ''Score per position''. These values locally refer to the hit as known from BLAST hits, so a high percent identity referring to a very small hit region can make this similarity show up as one of the first hits, as shown in the example. Checking '''Group by Genome''' will aggregate all hits to features in the same genome. A blue box will mark hits that belong to the same genome. After selecting the right values, you can press the button '''Resubmit''' to change the evidence view. [[Image:EvidenceFil1.png]] == Tabular Protein Evidence == Activate the second tab of the large page-spanning [[WebComponents/Tabview|TabView]] to see the tabular view of the evidence. You will find most of the information already shown in the visual view, presented differently and enriched with some additional information. Added are the '''Identical Proteins''' and the '''Functionally coupled''' sections, while '''Location''' information is not presented in this tab. === Similarities === The similarity [[WebComponents/Table|table]] lists hits to similar features in the SEED and other databases, as described at [[SEED_Viewer_Manual/Evidence#Visual Protein Evidence|Visual Protein Evidence]]. Each row in the table represents a hit. The first column provides a checkbox to select a hit feature. Again, the buttons '''Align Selected''' and '''FASTA Download Selected''' are present and can be used to get to a TCoffee [[SEED_Viewer_Manual/AlignSeqs|alignment page]] or download the protein sequences of the selected features in FASTA format. The two buttons in the column header allow mass selection of the features. '''All''' will select all features visible in the table, '''check to last checked''' lets you select all features up to a selected feature in the [[WebComponents/Table|table]]. The ID of the hit features, as well as a link to the [[SEED_Viewer_Manual/Annotation|annotation page]] is displayed in the column '''Similar FIG Sequence'''. The next four columns describe information to the hit regions of the query and hit features ('''E-value''', '''Percent Identity''', '''Region in Query peg''' and '''Region in Similar Sequence'''). The '''Organism''' of the hit peg and its '''Function''' are shown in the next two columns. If the function is different from the function of the query feature, it is colored. Same function in the table will get the same color. '''Associated Subsystems'' of the feature are displayed in the next column. If the feature is not associated to a subsystem, you will find the text ''None added'' in the cell. There are three '''Evidence Codes''' that can be found in the last column. ''ISU'' means that the feature is unique in a cell of a subsystem. This means that there is no other feature in the genome that is thought to have the same function. ICW(number) means the feature is clustered with ''number'' features in the genome. ''FF'' says that it is in a [[Glossary#FIGfam|FIGfam]]. The [[WebComponents/Table|table]] can be exported via the button '''export table''' that can be found on top of the table. [[Image:EvidenceSims2.png]] You can filter and sort the table using the [[WebComponents/Tabview|TabView]] above the table. The second tab, '''Sims Filter''' works the same way as described for the Similarities in the [[SEED_Viewer_Manual/Evidence#Visual Protein Evidence|Visual Protein Evidence]]. The first tab '''Edit Columns''' contains a number of columns with additional information that can be added to the display of the table ([[Glossary#FIGfams|FIGfams]], different aliases to other databases and many others). Just choose a column name, press the arrow to put it into the right field and it will add it to the table. [[Image:EvidenceFilter.png]] === Domains === This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the whole length of the protein). The [[WebComponents/Table|table]] lists the '''Domain DB''' (the database for the domain that was hit), the '''ID''' in the domain database, the '''Name''' of the domain, the '''Location''' of the hit in the selected feature, the '''Score''' for the hit against the domain, as well as the '''Function''' of the domain. The table can be exported using the '''export table''' button. Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]]''' in the menu bar. [[Image:EvidenceDomTable.png]] === Identical Proteins === '''Essentially Identical Proteins''' are proteins that share a common sequence, but the start position of the proteins may vary a little. This definition was made because in different databases or close strains of organisms, it often happens that a protein is present, but the start position may be shifted in the finding genes step. So essentially, this table shows aliases of the feature that were based on protein identity. The first column of the [[WebComponents/Table|table]] shows the '''Database''' the alias can be found in, while the second column ('''ID''') offers the alias name and a link to the protein in the respective database. The following two columns describe the '''Organism''' and the '''Assignment''' for the feature for the alias. [[Image:EvidenceEIPs.png]] === Functionally Coupled === This [[WebComponents/Table|table]] lists all [[Glossary#Functional coupling|functionally coupled]] genes in the organism. You can see the '''Score''', the '''ID''' of the feature and the '''Function''' of the feature. [[Image:EvidenceFCs.png]] 48fab8aa381cb915ea2e1c753f3dbeb2b431b267 0 1502 2434 2430 2008-12-08T13:30:31Z DanielaBartels 10 /* Similarities */ wikitext text/x-wiki The Evidence Page is divided into two parts via a [[WebComponents/Tabview|TabView]]: The '''Visual Protein Evidence''' and the '''Tabular Protein Evidence'''. If you are logged in and the feature belongs to your private genome, this page will have additional options for you to annotate the feature. These are described [[SEED_Viewer_Manual/Editing_Capabilities/Evidence|here]]. == Visual Protein Evidence == After loading the Evidence Page, the first tab of the [[WebComponents/Tabview|TabView]] is selected. It visually shows different pre-computed tool results for the given feature. In this view, you can see evidence for ''Location'' of the product of the gene in the cell, evidence for protein ''Domains'' and evidence that show ''Similarities'' to other features. === Location === '''Location''' stand for location of the product of the feature in the cell. This section presents output for tools that look for transmembrane helices (TM) or signal peptides (SP) in the feature. In the example, you can see five transmembrane helices in the protein identified via the Phobius tool. They are visualized as little boxes, and their location on the line depicts the location of the transmembrane helices in the protein. [[Image:EvidenceLocation.png]] === Domains === This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the full length of the protein). Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]]''' in the menu bar. [[Image:EvidenceDomain.png]] === Similarities === This section graphically lists evidence for similarities to other features in the SEED and other databases. The '''E-Value Key''' shown on the top defines the colors that are used to display different E-Value ranges for the similarities to the hit features. Hovering over the E-Value Key shows the value range for each color. Each similarity is represented by two bars, showing the alignment of the similarity. The first bar is the '''query''' feature, the second the '''hit''' feature. The abbreviation in front of this bar informs you about the organism the hit feature is in. Hover over the abbreviation to get the complete organism name. To the right of the checkbox you can find the [[Glossary#Functional role|functional role]] of the hit feature. The length of the outside box shows the complete length of the respective sequence. The color of the outside box represents the range of the evalue score according to the E-Value Key bar. The length of the inner (white) box depicts the actual section of the sequence the similarity to the other feature is in. Hovering over the box will show you some information about the hit feature (see tooltip graphics below), including the [[Glossary#Functional role|functional role]], the [[Glossary#Subsystem|subsystems]] and some values describing the hit area. If you check some of the checkboxes in front of the [[Glossary#Functional role|functional role]] descriptions of the hit genes, you can access two functions via the buttons on top of the Similarity graphics. The button '''Align Selected''' leads to an [[SEED_Viewer_Manual/AlignSeqs|alignment page]] showing a TCoffee alignment for the selected features. '''FASTA Download Selected''' lets you download the selected sequences in aminoacid FASTA format. [[Image:EvidenceSims1.png]] [[Image:EvidenceHoverSim.png]] To change the evidence view with respect to the sorting and the filtering of the hits, you can find a little control box on top of the similarity graphics. '''Max Sims''' is the number of similarities that are listed on the page. '''Max E-Value''' filters out all similarities that have a higher E-Value than stated here. In the little combo box below these two values, you can decide to see only hits against the SEED database ('''Just FIG IDs'''), or also against other databases ('''Show all Databases'''). You can '''Sort''' the '''Results By''' ''Score'', ''Percent Identity'' (default) or ''Score per position''. These values locally refer to the hit as known from BLAST hits, so a high percent identity referring to a very small hit region can make this similarity show up as one of the first hits, as shown in the example. Checking '''Group by Genome''' will aggregate all hits to features in the same genome. A blue box will mark hits that belong to the same genome. After selecting the right values, you can press the button '''Resubmit''' to change the evidence view. [[Image:EvidenceFil1.png]] == Tabular Protein Evidence == Activate the second tab of the large page-spanning [[WebComponents/Tabview|TabView]] to see the tabular view of the evidence. You will find most of the information already shown in the visual view, presented differently and enriched with some additional information. Added are the '''Identical Proteins''' and the '''Functionally coupled''' sections, while '''Location''' information is not presented in this tab. === Similarities === The similarity [[WebComponents/Table|table]] lists hits to similar features in the SEED and other databases, as described at [[SEED_Viewer_Manual/Evidence#Visual Protein Evidence|Visual Protein Evidence]]. Each row in the table represents a hit. The first column provides a checkbox to select a hit feature. Again, the buttons '''Align Selected''' and '''FASTA Download Selected''' are present and can be used to get to a TCoffee [[SEED_Viewer_Manual/AlignSeqs|alignment page]] or download the protein sequences of the selected features in FASTA format. The two buttons in the column header allow mass selection of the features. '''All''' will select all features visible in the table, '''check to last checked''' lets you select all features up to a selected feature in the [[WebComponents/Table|table]]. The ID of the hit features, as well as a link to the [[SEED_Viewer_Manual/Annotation|annotation page]] is displayed in the column '''Similar FIG Sequence'''. The next four columns describe information to the hit regions of the query and hit features ('''E-value''', '''Percent Identity''', '''Region in Query peg''' and '''Region in Similar Sequence'''). The '''Organism''' of the hit peg and its '''Function''' are shown in the next two columns. If the function is different from the function of the query feature, it is colored. Same function in the table will get the same color. '''Associated Subsystems'' of the feature are displayed in the next column. If the feature is not associated to a subsystem, you will find the text ''None added'' in the cell. There are three '''Evidence Codes''' that can be found in the last column. ''ISU'' means that the feature is unique in a cell of a subsystem. This means that there is no other feature in the genome that is thought to have the same function. ICW(number) means the feature is clustered with ''number'' features in the genome. ''FF'' says that it is in a [[Glossary#FIGfam|FIGfam]]. The [[WebComponents/Table|table]] can be exported via the button '''export table''' that can be found on top of the table. [[Image:EvidenceSims2.png]] You can filter and sort the table using the [[WebComponents/Tabview|TabView]] above the table. The second tab, '''Sims Filter''' works the same way as described for the Similarities in the [[SEED_Viewer_Manual/Evidence#Visual Protein Evidence|Visual Protein Evidence]]. The first tab '''Edit Columns''' contains a [[WebComponents/ListSelect]] with a number of columns with additional information that can be added to the display of the table ([[Glossary#FIGfams|FIGfams]], different aliases to other databases and many others). Just choose a column name, press the arrow to put it into the right field and it will add it to the table. [[Image:EvidenceFilter.png]] === Domains === This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the whole length of the protein). The [[WebComponents/Table|table]] lists the '''Domain DB''' (the database for the domain that was hit), the '''ID''' in the domain database, the '''Name''' of the domain, the '''Location''' of the hit in the selected feature, the '''Score''' for the hit against the domain, as well as the '''Function''' of the domain. The table can be exported using the '''export table''' button. Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]]''' in the menu bar. [[Image:EvidenceDomTable.png]] === Identical Proteins === '''Essentially Identical Proteins''' are proteins that share a common sequence, but the start position of the proteins may vary a little. This definition was made because in different databases or close strains of organisms, it often happens that a protein is present, but the start position may be shifted in the finding genes step. So essentially, this table shows aliases of the feature that were based on protein identity. The first column of the [[WebComponents/Table|table]] shows the '''Database''' the alias can be found in, while the second column ('''ID''') offers the alias name and a link to the protein in the respective database. The following two columns describe the '''Organism''' and the '''Assignment''' for the feature for the alias. [[Image:EvidenceEIPs.png]] === Functionally Coupled === This [[WebComponents/Table|table]] lists all [[Glossary#Functional coupling|functionally coupled]] genes in the organism. You can see the '''Score''', the '''ID''' of the feature and the '''Function''' of the feature. [[Image:EvidenceFCs.png]] 8ea7c1e12908d3bee936beb665dc13945fb1b320 2435 2434 2008-12-08T13:31:22Z DanielaBartels 10 /* Similarities */ wikitext text/x-wiki The Evidence Page is divided into two parts via a [[WebComponents/Tabview|TabView]]: The '''Visual Protein Evidence''' and the '''Tabular Protein Evidence'''. If you are logged in and the feature belongs to your private genome, this page will have additional options for you to annotate the feature. These are described [[SEED_Viewer_Manual/Editing_Capabilities/Evidence|here]]. == Visual Protein Evidence == After loading the Evidence Page, the first tab of the [[WebComponents/Tabview|TabView]] is selected. It visually shows different pre-computed tool results for the given feature. In this view, you can see evidence for ''Location'' of the product of the gene in the cell, evidence for protein ''Domains'' and evidence that show ''Similarities'' to other features. === Location === '''Location''' stand for location of the product of the feature in the cell. This section presents output for tools that look for transmembrane helices (TM) or signal peptides (SP) in the feature. In the example, you can see five transmembrane helices in the protein identified via the Phobius tool. They are visualized as little boxes, and their location on the line depicts the location of the transmembrane helices in the protein. [[Image:EvidenceLocation.png]] === Domains === This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the full length of the protein). Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]]''' in the menu bar. [[Image:EvidenceDomain.png]] === Similarities === This section graphically lists evidence for similarities to other features in the SEED and other databases. The '''E-Value Key''' shown on the top defines the colors that are used to display different E-Value ranges for the similarities to the hit features. Hovering over the E-Value Key shows the value range for each color. Each similarity is represented by two bars, showing the alignment of the similarity. The first bar is the '''query''' feature, the second the '''hit''' feature. The abbreviation in front of this bar informs you about the organism the hit feature is in. Hover over the abbreviation to get the complete organism name. To the right of the checkbox you can find the [[Glossary#Functional role|functional role]] of the hit feature. The length of the outside box shows the complete length of the respective sequence. The color of the outside box represents the range of the evalue score according to the E-Value Key bar. The length of the inner (white) box depicts the actual section of the sequence the similarity to the other feature is in. Hovering over the box will show you some information about the hit feature (see tooltip graphics below), including the [[Glossary#Functional role|functional role]], the [[Glossary#Subsystem|subsystems]] and some values describing the hit area. If you check some of the checkboxes in front of the [[Glossary#Functional role|functional role]] descriptions of the hit genes, you can access two functions via the buttons on top of the Similarity graphics. The button '''Align Selected''' leads to an [[SEED_Viewer_Manual/AlignSeqs|alignment page]] showing a TCoffee alignment for the selected features. '''FASTA Download Selected''' lets you download the selected sequences in aminoacid FASTA format. [[Image:EvidenceSims1.png]] [[Image:EvidenceHoverSim.png]] To change the evidence view with respect to the sorting and the filtering of the hits, you can find a little control box on top of the similarity graphics. '''Max Sims''' is the number of similarities that are listed on the page. '''Max E-Value''' filters out all similarities that have a higher E-Value than stated here. In the little combo box below these two values, you can decide to see only hits against the SEED database ('''Just FIG IDs'''), or also against other databases ('''Show all Databases'''). You can '''Sort''' the '''Results By''' ''Score'', ''Percent Identity'' (default) or ''Score per position''. These values locally refer to the hit as known from BLAST hits, so a high percent identity referring to a very small hit region can make this similarity show up as one of the first hits, as shown in the example. Checking '''Group by Genome''' will aggregate all hits to features in the same genome. A blue box will mark hits that belong to the same genome. After selecting the right values, you can press the button '''Resubmit''' to change the evidence view. [[Image:EvidenceFil1.png]] == Tabular Protein Evidence == Activate the second tab of the large page-spanning [[WebComponents/Tabview|TabView]] to see the tabular view of the evidence. You will find most of the information already shown in the visual view, presented differently and enriched with some additional information. Added are the '''Identical Proteins''' and the '''Functionally coupled''' sections, while '''Location''' information is not presented in this tab. === Similarities === The similarity [[WebComponents/Table|table]] lists hits to similar features in the SEED and other databases, as described at [[SEED_Viewer_Manual/Evidence#Visual Protein Evidence|Visual Protein Evidence]]. Each row in the table represents a hit. The first column provides a checkbox to select a hit feature. Again, the buttons '''Align Selected''' and '''FASTA Download Selected''' are present and can be used to get to a TCoffee [[SEED_Viewer_Manual/AlignSeqs|alignment page]] or download the protein sequences of the selected features in FASTA format. The two buttons in the column header allow mass selection of the features. '''All''' will select all features visible in the table, '''check to last checked''' lets you select all features up to a selected feature in the [[WebComponents/Table|table]]. The ID of the hit features, as well as a link to the [[SEED_Viewer_Manual/Annotation|annotation page]] is displayed in the column '''Similar FIG Sequence'''. The next four columns describe information to the hit regions of the query and hit features ('''E-value''', '''Percent Identity''', '''Region in Query peg''' and '''Region in Similar Sequence'''). The '''Organism''' of the hit peg and its '''Function''' are shown in the next two columns. If the function is different from the function of the query feature, it is colored. Same function in the table will get the same color. '''Associated Subsystems'' of the feature are displayed in the next column. If the feature is not associated to a subsystem, you will find the text ''None added'' in the cell. There are three '''Evidence Codes''' that can be found in the last column. ''ISU'' means that the feature is unique in a cell of a subsystem. This means that there is no other feature in the genome that is thought to have the same function. ICW(number) means the feature is clustered with ''number'' features in the genome. ''FF'' says that it is in a [[Glossary#FIGfam|FIGfam]]. The [[WebComponents/Table|table]] can be exported via the button '''export table''' that can be found on top of the table. [[Image:EvidenceSims2.png]] You can filter and sort the table using the [[WebComponents/Tabview|TabView]] above the table. The second tab, '''Sims Filter''' works the same way as described for the Similarities in the [[SEED_Viewer_Manual/Evidence#Visual Protein Evidence|Visual Protein Evidence]]. The first tab '''Edit Columns''' contains a [[WebComponents/ListSelect|List Select]] with a number of columns with additional information that can be added to the display of the table ([[Glossary#FIGfams|FIGfams]], different aliases to other databases and many others). Just choose a column name, press the arrow to put it into the right field and it will add it to the table. [[Image:EvidenceFilter.png]] === Domains === This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the whole length of the protein). The [[WebComponents/Table|table]] lists the '''Domain DB''' (the database for the domain that was hit), the '''ID''' in the domain database, the '''Name''' of the domain, the '''Location''' of the hit in the selected feature, the '''Score''' for the hit against the domain, as well as the '''Function''' of the domain. The table can be exported using the '''export table''' button. Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]]''' in the menu bar. [[Image:EvidenceDomTable.png]] === Identical Proteins === '''Essentially Identical Proteins''' are proteins that share a common sequence, but the start position of the proteins may vary a little. This definition was made because in different databases or close strains of organisms, it often happens that a protein is present, but the start position may be shifted in the finding genes step. So essentially, this table shows aliases of the feature that were based on protein identity. The first column of the [[WebComponents/Table|table]] shows the '''Database''' the alias can be found in, while the second column ('''ID''') offers the alias name and a link to the protein in the respective database. The following two columns describe the '''Organism''' and the '''Assignment''' for the feature for the alias. [[Image:EvidenceEIPs.png]] === Functionally Coupled === This [[WebComponents/Table|table]] lists all [[Glossary#Functional coupling|functionally coupled]] genes in the organism. You can see the '''Score''', the '''ID''' of the feature and the '''Function''' of the feature. [[Image:EvidenceFCs.png]] 8ed8f22d69f4b1d022890274e0d7e8b91feddd2e 0 1611 2436 2008-12-08T13:39:35Z DanielaBartels 10 wikitext text/x-wiki == List Select == [Image:ListSelect.png] 515c7da4fe111c6561047a3c4b1109e1c96f9b5d 2437 2436 2008-12-08T13:39:47Z DanielaBartels 10 /* List Select */ wikitext text/x-wiki == List Select == [[Image:ListSelect.png]] cfab7181481e866000b69aa9051bae43063423ec 2439 2437 2008-12-08T13:49:12Z DanielaBartels 10 /* List Select */ wikitext text/x-wiki == List Select == This Component is used to select a number of items from a list. Usually, it is bound to a table where it adds additional columns from the list. To select an item to add, mark the item and then the right arrow to put it into the right list. To remove it, mark it in the right list and click the left button to put it back. The table the list select is bound to should update automatically. [[Image:ListSelect.png]] a1ac279c551018600c9bbe5509df0bcea76c5793 6 1612 2438 2008-12-08T13:40:09Z DanielaBartels 10 wikitext text/x-wiki da39a3ee5e6b4b0d3255bfef95601890afd80709 0 1613 2440 2008-12-12T10:20:41Z DanielaBartels 10 wikitext text/x-wiki <img src="http://www.theseed.org/w/images/0/04/ContigView1.png" width="594" height="186" border="0" usemap="#map" /> <map name="map"> <!-- #$-:Image Map file created by GIMP Imagemap Plugin --> <!-- #$-:GIMP Imagemap Plugin by Maurits Rijk --> <!-- #$-:Please do not edit lines starting with "#$" --> <!-- #$VERSION:2.0 --> <!-- #$AUTHOR:Daniela Bartels --> <area shape="rect" coords="230,36,367,58" href="www.google.de" /> </map> 27bc84d3e9ab7d0a3bf7998f2791ce6f7cc8e1f3 2441 2440 2008-12-12T10:22:28Z DanielaBartels 10 wikitext text/x-wiki <img src='http://www.theseed.org/w/images/0/04/ContigView1.png' width='594' height='186' border='0' usemap='#map' /> <map name='map'> <area shape='rect' coords='230,36,367,58' href='www.google.de' /> </map> 203da8d0fc4d93c13637cf2ea140f380f5cd7ae2 2442 2441 2008-12-12T10:23:33Z DanielaBartels 10 wikitext text/x-wiki <img src="http://www.theseed.org/w/images/0/04/ContigView1.png" usemap="#map" /> <map name='map'> <area shape='rect' coords='230,36,367,58' href='www.google.de' /> </map> 6d685e31babde75ae3af171ba4d899fe667b280d 0 1517 2445 2400 2008-12-12T14:13:22Z DanielaBartels 10 /* Scenarios */ wikitext text/x-wiki == Subsystems == A [[Glossary#Subsystem|subsystem]] is a collection of [[Glossary#Functional role|functional roles]] that are associated to each other in a system. Such a system can for example be a metabolic pathway or a component of a cell like a secretion system. The subsystem page in the SeedViewer is divided into different parts via a [[WebComponents/Tabview|TabView]]. The TabView can consist of 3-5 tabs. The first tab shows a '''Diagram''' of the subsystem, the second tab displays a [[WebComponents/Table|table]] with the '''Functional Roles''' present in the subsystem. The '''Spreadsheet''' relating the functional roles in the subsystem to features in genomes can be found in the third tab. The fourth and fifth tab show a description and additional notes to a subsystem. They only appear if a subsystem has a description / notes. The last tab displays the [[Glossary#Scenarios|Scenarios]] for the subsystem. === Diagram === The subsystem diagram shows the connections between the functional roles in a subsystem. The boxes represent the functional roles via their abbreviations. The circles are connecting intermediates, that are described in the table which is part of the diagram. The functional roles in the diagram can be colored according to their presence in a genome. Click the button '''Color Diagram''' to get a combo box with all genomes in the subsystem. Select your genome of interest and press '''do coloring'''. The boxes for the functional roles defined for that genome will now be colored in green. [[Image:SubsystemDiagram.png]] === Functional Roles === This [[WebComponents/Table|table]] lists all functional roles present in the subsystem. The first column shows '''Group Aliases''' for the functional role. Functional roles can be aggregated in groups (subsets). Subset names that start with a '*' contain alternative ways to implement a function. The abbreviation ('''Abbrev.''') for a functional role must be unique for the functional roles in the subsystem. It is used in different displays like the Diagram or the Speadsheet. The third column lists the full name of the functional role. EC-Numbers are often part of the functional role (for enzymes), and are stated in parentheses after the name of the functional role. The following two columns deal with reactions a functional role is connected to. Clicking on the link opens a new window showing the KEGG reaction. Next to annotator-curated KEGG reactions, we show the KEGG reactions of the curation effort of the [[SEED_People#Hope College|Hope College]] team that collaborates with the SEED. GeneOntology (GO) links are displayed in the next column. The links point to the GO-number in GeneOntology's Amigo-Tool. The last column can contain literature (PubMed IDs) that describes the functional role in detail. If present, you will find a link to PubMed in this column. [[Image:SubsystemFRs.png]] === Spreadsheet === The subsystem spreadsheet displays the features that are assigned with the functional roles in all organisms that are part of the subsystem. The organisms are displayed in the first column. The links lead to the [[SEED_Viewer_Manual/OrganismPage|Organism Page]]. The column header includes a filter option for the organism, doing an infix search on the organism name. The '''Domain''' (Bacterial, Archaeal or Eukaryote) of the organism is shown in the second column. For each organism in the spreadsheet, a '''Variant Code''' is assigned. Usually, there is more than one way to fulfill a subsystem. Metabolic pathways can have alternatives, or parts of the pathway may be present or absent in an organism. [[Glossary#Variant Code|Variant Codes]] are assigned to the organism to express this behavior. There are two special Variant Codes: '''0''' and '''-1'''. The Variant Code '''-1''' means that the organism has no active variant of this subsystem, it is not implement this organism. '''0''' means that the curator has not yet assigned a variant to the genome. Due to the flow of newly sequenced genomes into the SEED, this variant code may show up sometimes. The next column is used to filter active or inactive variants. If you want to see only the active ones (default), enter '''yes''' into the filter in the column header. For seeing only the not active ones, enter '''no'''. No input in this field will show all variants. All following columns in the table show the features in the organisms that are assigned with functional roles. The column headers display the abbreviations of the functional roles (see Functional Roles Table). Hovering over a column header will show a tooltip with the full name of the role. The feature entries in the cells for the functional roles are linked to the [[SEED_Viewer_Manual/Annotation|Annotation Page]] for that feature. There can be multiple features in a cell, as some functions are implemented by more that one feature in an organism. The control table above the spreadsheet table lets you change the display in the table: Functional Roles that belong to a subset starting with a '*', meaning they are alternatives for a function, are collapsed in the spreadsheet by default. If you want to expand the subsets, you can do so by checking '''expanded''' in the '''Subsets''' column. The feature entries in the spreadsheet can be colored according to different metaphors using the second column ('''Coloring''') of the table. By default, the features are colored '''by cluster'''. In this case, it is computed which features are close by on the genomic sequence, meaning they cluster. Each computed cluster gets its own color. These colors only have a meaning per genome, meaning that a yellow cluster in one genome has no connection to a yellow cluster in the next genome. Another way to cluster the features are different kinds of attributes. Check the radio box for '''by attribute''' and choose an attribute in the drop down menu. Press '''update''' to change the display. [[Image:SubsystemSpreadsheet.png]] === Description === The description of a subsystem gives an overview of the functional roles and their connections in the subsystem. It can give some background information about the system, what organisms it is usually found in and other facts that are of interest. === Additional Notes === As the description already gives an overview over the subsystem, additional notes can be found here. The notes usually refer to specific properties of some organisms or organism groups, genes that are missing but should be there and other details that might be useful for the interested user. === Scenarios === The table shows all scenarios that occur in the subsystem. You can see the scenario name, the '''Input Compounds''', the '''Output Compounds''' and a checkbox to decide if you want to see the scenario painted on the [http://www.genome.jp/kegg/ KEGG] map below. If you change the selection of scenarios to paint on the map, click the button '''Paint Map(s)''' to reload the map. You can also select an organism to highlight on the map. Therefore, click the '''Select Organism''' button to get an [[SEED_Viewer_Manual/OrganismSelect|Organism Select]]. After choosing an organism, click the button '''Highlight Reactions for Organism''' to mark the enzymes present in the organism with black boxes. [[Image:SubsystemScenTabs.png]] The [http://www.genome.jp/kegg/ KEGG] map is the first tab of a [[WebComponents/Tabview|TabView]]. The header of the tab includes a link to the map at [http://www.genome.jp/kegg/ KEGG]. Each enzyme in the map is painted with all colors of the scenarios it is part of. A color legend is presented on the right side of the map. The second tab of the [[WebComponents/Tabview|TabView]] shows all reactions that are not shown on the map, but are part of the subsystem. [[Image:SubsystemScenarios.png]] 651976db4235025f99c7fd8c0f97158e7b29fc7e 0 1466 2446 2380 2008-12-12T15:02:52Z DanielaBartels 10 /* Main pages of the SeedViewer */ wikitext text/x-wiki == Overview of the pages in the SeedViewer == [[Image:SeedViewerOverview.png]] == Main pages of the SeedViewer == '''[[SEED_Viewer_Manual|Home Page]]''' '''[[SEED_Viewer_Manual/Menu|Menu]]''' '''[[SEED_Viewer_Manual/Annotation|Annotation]]''' '''[[SEED_Viewer_Manual/AlignSeqs|Alignment Page]]''' '''[[SEED_Viewer_Manual/BLASTOrganism|BLAST against an organism]]''' '''[[SEED_Viewer_Manual/BLASTDotPlot|BLAST Dot Plot]]''' '''[[SEED_Viewer_Manual/DownloadOrganism|Download Organism]]''' '''[[SEED_Viewer_Manual/GenomeBrowser|Browse Genome]]''' '''[[SEED_Viewer_Manual/CompareMetabolicReconstruction|Compare Metabolic Reconstruction]]''' '''[[SEED_Viewer_Manual/ContigView|Contig View]]''' '''[[SEED_Viewer_Manual/Evidence|Evidence]]''' '''[[SEED_Viewer_Manual/FIGfams|FIGfams]]''' '''[[SEED_Viewer_Manual/FIGfamsRelease|FIGfam Release]]''' '''[[SEED_Viewer_Manual/FIGfamViewer|FIGfam Viewer]]''' '''[[SEED_Viewer_Manual/FunctionalRoles|Functional Role]]''' '''[[SEED_Viewer_Manual/HomologClusters|Homolog Clusters]]''' '''[[SEED_Viewer_Manual/KEGG|KEGG Page]]''' '''[[SEED_Viewer_Manual/MultiGenomeCompare|Multi Genome Compare]]''' '''[[SEED_Viewer_Manual/OrganismPage|Organism Page]]''' '''[[SEED_Viewer_Manual/OrganismSelect|Organism Select]]''' '''[[SEED_Viewer_Manual/SearchGene|Search Gene]]''' '''[[SEED_Viewer_Manual/Scenarios|Scenarios]]''' '''[[SEED_Viewer_Manual/ShowSeqs|Sequence]]''' '''[[SEED_Viewer_Manual/Subsystems|Subsystems Page]]''' 7e01b8424e76acb634c983609717bfe00c02758e 6 1615 2447 2008-12-12T15:04:36Z DanielaBartels 10 wikitext text/x-wiki da39a3ee5e6b4b0d3255bfef95601890afd80709 0 1463 2448 2163 2008-12-15T11:30:46Z DanielaBartels 10 /* (1) [[SEED_Viewer_Manual/Menu|The menu]] */ wikitext text/x-wiki The SEED is a framework to support comparative analysis and annotation of genomes. The SEED Viewer allows you to explore the curated genomes that have been produced by a cooperative effort that includes Fellowship for Interpretation of Genomes (FIG), Argonne National Laboratory, the University of Chicago and teams from a number of other institutions. These pages will cover the usage of the different pages within the Seed Viewer. An overview of the main pages in the SeedViewer can be found in the '''[[SEED_Viewer_Manual/Contents|Contents Page]]'''. == Home == The home page of the seedviewer offers you several entry points to explore the data in the [[Home_of_the_SEED|SEED]]. Common components of a web page in the seedviewer are the following. The image below depicts the locations of the components: === (1) [[SEED_Viewer_Manual/Menu|The menu]] === The menu is a green bar located under the SeedViewer Logo. Hovering over the menu will show you submenus that are relevant for the page you are viewing. The categories '''[[SEED_Viewer_Manual/Menu#Navigate_Menu|Navigate]]''' and '''[[SEED_Viewer_Manual/Menu#Help_Menu|Help]]''' will always be present on each page. Other menu categories are added dependent on the context of the page. Click [[SEED_Viewer_Manual/Menu|here]] to learn more about using the menu. === (2) [[SEED_Viewer_Manual/Find|Find Window]] === The Find window allows you to search for keywords or ids. To learn more about the find window, click [[SEED_Viewer_Manual/Find|here]]. === (3) [[WebComponents/Login|Login Box]] === Some actions may require a user to get a user account and log in. This is necessary for viewing private organisms a user has uploaded to the [[RAST_Tutorial|RAST]]. You can create a login by clicking on '''Register''' in the '''Help''' menu. To learn more about user management click [[SEED_Viewer_Manual/UserManagement|here]]. === (4) Body of the Page === The home page allows you to specifically search the SEED data using five categories. They are presented in a [[WebComponents/Tabview|TabView]] at the bottom of the Home page: '''a) Organisms''' Select an organism of interest in the [[SEED_Viewer_Manual/OrganismSelect|Organism Select]] and press the button '''select'''. This will lead to the [[SEED_Viewer_Manual/OrganismPage|Organism Page]] of that organism. '''b) Subsystems''' Selecting a subsystem in the Select Box and clicking '''Select''' will lead you to a [[SEED_Viewer_Manual/Subsystems|Subsystem Page]]. You can narrow the selection by typing in a part of the subsystem name into the field on top of the select box. '''c) ID search''' If you know the ID of a gene or protein you're interested in, you can directly type it into this field and press '''ID Search'''. The ID can be a SEED (fig) id as well as many other types of IDs from other databases (e.g. GenBank, KEGG, SwissProt, UniProt and others). These IDs are saved in the SEED as [[Glossary#Aliases|Aliases]]. '''d) Text search''' You can search for any type of data in this field. This includes search for Organisms, Subsystems, IDs as well as Functional Roles of proteins. It should be used carefully, as the search is an infix search and can take very long (e.g. if you only type in one letter it may take forever). If you already know that you are looking for, e.g. a subsystem, it would be faster to use the Subsystems tab. '''e) BLAST''' This tab offers the option to search a DNA or protein sequence against an organism in the SEED. It is described in more detail [[SEED_Viewer_Manual/BLASTOrganism|here]]. [[Image:Home1.png]] 2a8af4207788732d76fe39ca2fe7430877d35c60 2449 2448 2008-12-15T11:33:06Z DanielaBartels 10 /* (2) [[SEED_Viewer_Manual/Find|Find Window]] */ wikitext text/x-wiki The SEED is a framework to support comparative analysis and annotation of genomes. The SEED Viewer allows you to explore the curated genomes that have been produced by a cooperative effort that includes Fellowship for Interpretation of Genomes (FIG), Argonne National Laboratory, the University of Chicago and teams from a number of other institutions. These pages will cover the usage of the different pages within the Seed Viewer. An overview of the main pages in the SeedViewer can be found in the '''[[SEED_Viewer_Manual/Contents|Contents Page]]'''. == Home == The home page of the seedviewer offers you several entry points to explore the data in the [[Home_of_the_SEED|SEED]]. Common components of a web page in the seedviewer are the following. The image below depicts the locations of the components: === (1) [[SEED_Viewer_Manual/Menu|The menu]] === The menu is a green bar located under the SeedViewer Logo. Hovering over the menu will show you submenus that are relevant for the page you are viewing. The categories '''[[SEED_Viewer_Manual/Menu#Navigate_Menu|Navigate]]''' and '''[[SEED_Viewer_Manual/Menu#Help_Menu|Help]]''' will always be present on each page. Other menu categories are added dependent on the context of the page. Click [[SEED_Viewer_Manual/Menu|here]] to learn more about using the menu. === (2) [[SEED_Viewer_Manual/Find|Find Window]] === On the right side of the menu bar you will find an input field labeled '''Find'''. The Find Window allows you to search the SEED data for keywords or ids. To learn more about the Find Window, click [[SEED_Viewer_Manual/Find|here]]. === (3) [[WebComponents/Login|Login Box]] === Some actions may require a user to get a user account and log in. This is necessary for viewing private organisms a user has uploaded to the [[RAST_Tutorial|RAST]]. You can create a login by clicking on '''Register''' in the '''Help''' menu. To learn more about user management click [[SEED_Viewer_Manual/UserManagement|here]]. === (4) Body of the Page === The home page allows you to specifically search the SEED data using five categories. They are presented in a [[WebComponents/Tabview|TabView]] at the bottom of the Home page: '''a) Organisms''' Select an organism of interest in the [[SEED_Viewer_Manual/OrganismSelect|Organism Select]] and press the button '''select'''. This will lead to the [[SEED_Viewer_Manual/OrganismPage|Organism Page]] of that organism. '''b) Subsystems''' Selecting a subsystem in the Select Box and clicking '''Select''' will lead you to a [[SEED_Viewer_Manual/Subsystems|Subsystem Page]]. You can narrow the selection by typing in a part of the subsystem name into the field on top of the select box. '''c) ID search''' If you know the ID of a gene or protein you're interested in, you can directly type it into this field and press '''ID Search'''. The ID can be a SEED (fig) id as well as many other types of IDs from other databases (e.g. GenBank, KEGG, SwissProt, UniProt and others). These IDs are saved in the SEED as [[Glossary#Aliases|Aliases]]. '''d) Text search''' You can search for any type of data in this field. This includes search for Organisms, Subsystems, IDs as well as Functional Roles of proteins. It should be used carefully, as the search is an infix search and can take very long (e.g. if you only type in one letter it may take forever). If you already know that you are looking for, e.g. a subsystem, it would be faster to use the Subsystems tab. '''e) BLAST''' This tab offers the option to search a DNA or protein sequence against an organism in the SEED. It is described in more detail [[SEED_Viewer_Manual/BLASTOrganism|here]]. [[Image:Home1.png]] 65f3d080dd3b5fc615293927e25638473e3a2df4 2450 2449 2008-12-15T11:34:04Z DanielaBartels 10 /* (2) [[SEED_Viewer_Manual/Find|Find Window]] */ wikitext text/x-wiki The SEED is a framework to support comparative analysis and annotation of genomes. The SEED Viewer allows you to explore the curated genomes that have been produced by a cooperative effort that includes Fellowship for Interpretation of Genomes (FIG), Argonne National Laboratory, the University of Chicago and teams from a number of other institutions. These pages will cover the usage of the different pages within the Seed Viewer. An overview of the main pages in the SeedViewer can be found in the '''[[SEED_Viewer_Manual/Contents|Contents Page]]'''. == Home == The home page of the seedviewer offers you several entry points to explore the data in the [[Home_of_the_SEED|SEED]]. Common components of a web page in the seedviewer are the following. The image below depicts the locations of the components: === (1) [[SEED_Viewer_Manual/Menu|The menu]] === The menu is a green bar located under the SeedViewer Logo. Hovering over the menu will show you submenus that are relevant for the page you are viewing. The categories '''[[SEED_Viewer_Manual/Menu#Navigate_Menu|Navigate]]''' and '''[[SEED_Viewer_Manual/Menu#Help_Menu|Help]]''' will always be present on each page. Other menu categories are added dependent on the context of the page. Click [[SEED_Viewer_Manual/Menu|here]] to learn more about using the menu. === (2) [[SEED_Viewer_Manual/Find|Find Window]] === On the right side of the menu bar you will find an input field with a '''find''' button in front of it. The Find Window allows you to search the SEED data for keywords or ids. To learn more about the search using the Find Window, click [[SEED_Viewer_Manual/Find|here]]. === (3) [[WebComponents/Login|Login Box]] === Some actions may require a user to get a user account and log in. This is necessary for viewing private organisms a user has uploaded to the [[RAST_Tutorial|RAST]]. You can create a login by clicking on '''Register''' in the '''Help''' menu. To learn more about user management click [[SEED_Viewer_Manual/UserManagement|here]]. === (4) Body of the Page === The home page allows you to specifically search the SEED data using five categories. They are presented in a [[WebComponents/Tabview|TabView]] at the bottom of the Home page: '''a) Organisms''' Select an organism of interest in the [[SEED_Viewer_Manual/OrganismSelect|Organism Select]] and press the button '''select'''. This will lead to the [[SEED_Viewer_Manual/OrganismPage|Organism Page]] of that organism. '''b) Subsystems''' Selecting a subsystem in the Select Box and clicking '''Select''' will lead you to a [[SEED_Viewer_Manual/Subsystems|Subsystem Page]]. You can narrow the selection by typing in a part of the subsystem name into the field on top of the select box. '''c) ID search''' If you know the ID of a gene or protein you're interested in, you can directly type it into this field and press '''ID Search'''. The ID can be a SEED (fig) id as well as many other types of IDs from other databases (e.g. GenBank, KEGG, SwissProt, UniProt and others). These IDs are saved in the SEED as [[Glossary#Aliases|Aliases]]. '''d) Text search''' You can search for any type of data in this field. This includes search for Organisms, Subsystems, IDs as well as Functional Roles of proteins. It should be used carefully, as the search is an infix search and can take very long (e.g. if you only type in one letter it may take forever). If you already know that you are looking for, e.g. a subsystem, it would be faster to use the Subsystems tab. '''e) BLAST''' This tab offers the option to search a DNA or protein sequence against an organism in the SEED. It is described in more detail [[SEED_Viewer_Manual/BLASTOrganism|here]]. [[Image:Home1.png]] c48017d665c8f80604f956139f503f773390ec38 2451 2450 2008-12-15T11:36:51Z DanielaBartels 10 /* (4) Body of the Page */ wikitext text/x-wiki The SEED is a framework to support comparative analysis and annotation of genomes. The SEED Viewer allows you to explore the curated genomes that have been produced by a cooperative effort that includes Fellowship for Interpretation of Genomes (FIG), Argonne National Laboratory, the University of Chicago and teams from a number of other institutions. These pages will cover the usage of the different pages within the Seed Viewer. An overview of the main pages in the SeedViewer can be found in the '''[[SEED_Viewer_Manual/Contents|Contents Page]]'''. == Home == The home page of the seedviewer offers you several entry points to explore the data in the [[Home_of_the_SEED|SEED]]. Common components of a web page in the seedviewer are the following. The image below depicts the locations of the components: === (1) [[SEED_Viewer_Manual/Menu|The menu]] === The menu is a green bar located under the SeedViewer Logo. Hovering over the menu will show you submenus that are relevant for the page you are viewing. The categories '''[[SEED_Viewer_Manual/Menu#Navigate_Menu|Navigate]]''' and '''[[SEED_Viewer_Manual/Menu#Help_Menu|Help]]''' will always be present on each page. Other menu categories are added dependent on the context of the page. Click [[SEED_Viewer_Manual/Menu|here]] to learn more about using the menu. === (2) [[SEED_Viewer_Manual/Find|Find Window]] === On the right side of the menu bar you will find an input field with a '''find''' button in front of it. The Find Window allows you to search the SEED data for keywords or ids. To learn more about the search using the Find Window, click [[SEED_Viewer_Manual/Find|here]]. === (3) [[WebComponents/Login|Login Box]] === Some actions may require a user to get a user account and log in. This is necessary for viewing private organisms a user has uploaded to the [[RAST_Tutorial|RAST]]. You can create a login by clicking on '''Register''' in the '''Help''' menu. To learn more about user management click [[SEED_Viewer_Manual/UserManagement|here]]. === (4) Body of the Page === The home page allows you to specifically search the SEED data using five categories. They are presented in a [[WebComponents/Tabview|TabView]] at the bottom of the Home page: '''a) Organisms''' Select an organism of interest in the [[SEED_Viewer_Manual/OrganismSelect|Organism Select]] and press the button '''select'''. This will lead to the [[SEED_Viewer_Manual/OrganismPage|Organism Page]] of that organism. '''b) Subsystems''' Selecting a subsystem in the Select Box and clicking '''Select''' will lead you to a [[SEED_Viewer_Manual/Subsystems|Subsystem Page]]. You can narrow the selection by typing in a part of the subsystem name into the field on top of the select box. '''c) ID search''' If you know the ID of a gene or protein you're interested in, you can directly specify it in this field and press '''ID Search'''. The ID can be a SEED (fig|...) ID as well as many other types of IDs from other databases (e.g. GenBank, KEGG, SwissProt, UniProt and others). These IDs are saved in the SEED as [[Glossary#Aliases|Aliases]]. '''d) Text search''' You can search for any type of data in this field. This includes search for Organisms, Subsystems, IDs as well as [[Glossary|Functional Role|Functional Roles]] of proteins. It should be used carefully, as the search is an infix search and can take very long (e.g. if you only type in one letter it may take forever). If you already know that you are looking for, e.g. a subsystem, it would be faster to use the Subsystems tab. '''e) BLAST''' This tab offers the option to search a DNA or protein sequence against an organism in the SEED. It is described in more detail [[SEED_Viewer_Manual/BLASTOrganism|here]]. [[Image:Home1.png]] f7484145453fb0167666f00d2906e89fcff50e93 2452 2451 2008-12-15T11:37:08Z DanielaBartels 10 /* (4) Body of the Page */ wikitext text/x-wiki The SEED is a framework to support comparative analysis and annotation of genomes. The SEED Viewer allows you to explore the curated genomes that have been produced by a cooperative effort that includes Fellowship for Interpretation of Genomes (FIG), Argonne National Laboratory, the University of Chicago and teams from a number of other institutions. These pages will cover the usage of the different pages within the Seed Viewer. An overview of the main pages in the SeedViewer can be found in the '''[[SEED_Viewer_Manual/Contents|Contents Page]]'''. == Home == The home page of the seedviewer offers you several entry points to explore the data in the [[Home_of_the_SEED|SEED]]. Common components of a web page in the seedviewer are the following. The image below depicts the locations of the components: === (1) [[SEED_Viewer_Manual/Menu|The menu]] === The menu is a green bar located under the SeedViewer Logo. Hovering over the menu will show you submenus that are relevant for the page you are viewing. The categories '''[[SEED_Viewer_Manual/Menu#Navigate_Menu|Navigate]]''' and '''[[SEED_Viewer_Manual/Menu#Help_Menu|Help]]''' will always be present on each page. Other menu categories are added dependent on the context of the page. Click [[SEED_Viewer_Manual/Menu|here]] to learn more about using the menu. === (2) [[SEED_Viewer_Manual/Find|Find Window]] === On the right side of the menu bar you will find an input field with a '''find''' button in front of it. The Find Window allows you to search the SEED data for keywords or ids. To learn more about the search using the Find Window, click [[SEED_Viewer_Manual/Find|here]]. === (3) [[WebComponents/Login|Login Box]] === Some actions may require a user to get a user account and log in. This is necessary for viewing private organisms a user has uploaded to the [[RAST_Tutorial|RAST]]. You can create a login by clicking on '''Register''' in the '''Help''' menu. To learn more about user management click [[SEED_Viewer_Manual/UserManagement|here]]. === (4) Body of the Page === The home page allows you to specifically search the SEED data using five categories. They are presented in a [[WebComponents/Tabview|TabView]] at the bottom of the Home page: '''a) Organisms''' Select an organism of interest in the [[SEED_Viewer_Manual/OrganismSelect|Organism Select]] and press the button '''select'''. This will lead to the [[SEED_Viewer_Manual/OrganismPage|Organism Page]] of that organism. '''b) Subsystems''' Selecting a subsystem in the Select Box and clicking '''Select''' will lead you to a [[SEED_Viewer_Manual/Subsystems|Subsystem Page]]. You can narrow the selection by typing in a part of the subsystem name into the field on top of the select box. '''c) ID search''' If you know the ID of a gene or protein you're interested in, you can directly specify it in this field and press '''ID Search'''. The ID can be a SEED (fig|...) ID as well as many other types of IDs from other databases (e.g. GenBank, KEGG, SwissProt, UniProt and others). These IDs are saved in the SEED as [[Glossary#Aliases|Aliases]]. '''d) Text search''' You can search for any type of data in this field. This includes search for Organisms, Subsystems, IDs as well as [[Glossary#Functional Role|Functional Roles]] of proteins. It should be used carefully, as the search is an infix search and can take very long (e.g. if you only type in one letter it may take forever). If you already know that you are looking for, e.g. a subsystem, it would be faster to use the Subsystems tab. '''e) BLAST''' This tab offers the option to search a DNA or protein sequence against an organism in the SEED. It is described in more detail [[SEED_Viewer_Manual/BLASTOrganism|here]]. [[Image:Home1.png]] 6af31284c252a2f196fa3bc086ea228784f3bc74 2453 2452 2008-12-15T11:37:43Z DanielaBartels 10 /* (4) Body of the Page */ wikitext text/x-wiki The SEED is a framework to support comparative analysis and annotation of genomes. The SEED Viewer allows you to explore the curated genomes that have been produced by a cooperative effort that includes Fellowship for Interpretation of Genomes (FIG), Argonne National Laboratory, the University of Chicago and teams from a number of other institutions. These pages will cover the usage of the different pages within the Seed Viewer. An overview of the main pages in the SeedViewer can be found in the '''[[SEED_Viewer_Manual/Contents|Contents Page]]'''. == Home == The home page of the seedviewer offers you several entry points to explore the data in the [[Home_of_the_SEED|SEED]]. Common components of a web page in the seedviewer are the following. The image below depicts the locations of the components: === (1) [[SEED_Viewer_Manual/Menu|The menu]] === The menu is a green bar located under the SeedViewer Logo. Hovering over the menu will show you submenus that are relevant for the page you are viewing. The categories '''[[SEED_Viewer_Manual/Menu#Navigate_Menu|Navigate]]''' and '''[[SEED_Viewer_Manual/Menu#Help_Menu|Help]]''' will always be present on each page. Other menu categories are added dependent on the context of the page. Click [[SEED_Viewer_Manual/Menu|here]] to learn more about using the menu. === (2) [[SEED_Viewer_Manual/Find|Find Window]] === On the right side of the menu bar you will find an input field with a '''find''' button in front of it. The Find Window allows you to search the SEED data for keywords or ids. To learn more about the search using the Find Window, click [[SEED_Viewer_Manual/Find|here]]. === (3) [[WebComponents/Login|Login Box]] === Some actions may require a user to get a user account and log in. This is necessary for viewing private organisms a user has uploaded to the [[RAST_Tutorial|RAST]]. You can create a login by clicking on '''Register''' in the '''Help''' menu. To learn more about user management click [[SEED_Viewer_Manual/UserManagement|here]]. === (4) Body of the Page === The home page allows you to specifically search the SEED data using five categories. They are presented in a [[WebComponents/Tabview|TabView]] at the bottom of the Home page: '''a) Organisms''' Select an organism of interest in the [[SEED_Viewer_Manual/OrganismSelect|Organism Select]] and press the button '''select'''. This will lead to the [[SEED_Viewer_Manual/OrganismPage|Organism Page]] of that organism. '''b) Subsystems''' Selecting a subsystem in the Select Box and clicking '''Select''' will lead you to a [[SEED_Viewer_Manual/Subsystems|Subsystem Page]]. You can narrow the selection by typing in a part of the subsystem name into the field on top of the select box. '''c) ID search''' If you know the ID of a gene or protein you're interested in, you can directly specify it in this field and press '''ID Search'''. The ID can be a SEED (fig|...) ID as well as many other types of IDs from other databases (e.g. GenBank, KEGG, SwissProt, UniProt and others). These IDs are saved in the SEED as [[Glossary#Aliases|Aliases]]. '''d) Text search''' You can search for any type of data in this field. This includes search for Organisms, Subsystems, IDs as well as [[Glossary#Functional role|Functional Roles]] of proteins. It should be used carefully, as the search is an infix search and can take very long (e.g. if you only type in one letter it may take forever). If you already know that you are looking for, e.g. a subsystem, it would be faster to use the Subsystems tab. '''e) BLAST''' This tab offers the option to search a DNA or protein sequence against an organism in the SEED. It is described in more detail [[SEED_Viewer_Manual/BLASTOrganism|here]]. [[Image:Home1.png]] caee3d23f434ba9fc49e3dffd97d189de8ba770a 2455 2453 2008-12-15T17:10:44Z DanielaBartels 10 /* (3) [[WebComponents/Login|Login Box]] */ wikitext text/x-wiki The SEED is a framework to support comparative analysis and annotation of genomes. The SEED Viewer allows you to explore the curated genomes that have been produced by a cooperative effort that includes Fellowship for Interpretation of Genomes (FIG), Argonne National Laboratory, the University of Chicago and teams from a number of other institutions. These pages will cover the usage of the different pages within the Seed Viewer. An overview of the main pages in the SeedViewer can be found in the '''[[SEED_Viewer_Manual/Contents|Contents Page]]'''. == Home == The home page of the seedviewer offers you several entry points to explore the data in the [[Home_of_the_SEED|SEED]]. Common components of a web page in the seedviewer are the following. The image below depicts the locations of the components: === (1) [[SEED_Viewer_Manual/Menu|The menu]] === The menu is a green bar located under the SeedViewer Logo. Hovering over the menu will show you submenus that are relevant for the page you are viewing. The categories '''[[SEED_Viewer_Manual/Menu#Navigate_Menu|Navigate]]''' and '''[[SEED_Viewer_Manual/Menu#Help_Menu|Help]]''' will always be present on each page. Other menu categories are added dependent on the context of the page. Click [[SEED_Viewer_Manual/Menu|here]] to learn more about using the menu. === (2) [[SEED_Viewer_Manual/Find|Find Window]] === On the right side of the menu bar you will find an input field with a '''find''' button in front of it. The Find Window allows you to search the SEED data for keywords or ids. To learn more about the search using the Find Window, click [[SEED_Viewer_Manual/Find|here]]. === (3) [[WebComponents/Login|Login Box]] === For using the publicly available data in the SEED no login or registration is required. If you wish to use our services [[RAST_Tutorial|RAST]] or [[MG_RAST_Tutorial|MG-RAST]], you need to obtain a login. That way, we can ensure that only you have access to your private data. This is also very helpfull for feedback and support. You can create a login by clicking on '''Register''' in the '''Help''' menu. To learn more about user management click [[SEED_Viewer_Manual/UserManagement|here]]. === (4) Body of the Page === The home page allows you to specifically search the SEED data using five categories. They are presented in a [[WebComponents/Tabview|TabView]] at the bottom of the Home page: '''a) Organisms''' Select an organism of interest in the [[SEED_Viewer_Manual/OrganismSelect|Organism Select]] and press the button '''select'''. This will lead to the [[SEED_Viewer_Manual/OrganismPage|Organism Page]] of that organism. '''b) Subsystems''' Selecting a subsystem in the Select Box and clicking '''Select''' will lead you to a [[SEED_Viewer_Manual/Subsystems|Subsystem Page]]. You can narrow the selection by typing in a part of the subsystem name into the field on top of the select box. '''c) ID search''' If you know the ID of a gene or protein you're interested in, you can directly specify it in this field and press '''ID Search'''. The ID can be a SEED (fig|...) ID as well as many other types of IDs from other databases (e.g. GenBank, KEGG, SwissProt, UniProt and others). These IDs are saved in the SEED as [[Glossary#Aliases|Aliases]]. '''d) Text search''' You can search for any type of data in this field. This includes search for Organisms, Subsystems, IDs as well as [[Glossary#Functional role|Functional Roles]] of proteins. It should be used carefully, as the search is an infix search and can take very long (e.g. if you only type in one letter it may take forever). If you already know that you are looking for, e.g. a subsystem, it would be faster to use the Subsystems tab. '''e) BLAST''' This tab offers the option to search a DNA or protein sequence against an organism in the SEED. It is described in more detail [[SEED_Viewer_Manual/BLASTOrganism|here]]. [[Image:Home1.png]] ebe689ca5645de6f56b10c964f5411cab84bbe8c 0 1616 2454 2008-12-15T11:55:35Z DanielaBartels 10 wikitext text/x-wiki == Annotation Clearing House == b57d8055098312a60d63d3f212aef9ed65359bc2 0 1375 2456 1485 2008-12-18T18:50:10Z Marland 16 wikitext text/x-wiki Have questions or comments about our applications? '''NMPDR''' Email: [mailto:help@nmpdr.org] Bugs: [mailto:bugs@nmpdr.org] '''RAST''' Email: [mailto:rast@mcs.anl.gov] '''Metagenomics RAST''' Email: [mailto:mg-rast@mcs.anl.gov] '''The SEED''' Email: [mailto:info@theseed.org] 8cb7ecfff87604a91c6e996ad1967409c44653b7 0 1374 2457 1628 2008-12-18T18:53:59Z Marland 16 wikitext text/x-wiki The people behind SEED are the following: * [http://www.thefig.info FIG] ** Ross Overbeek ** Veronika Vonstein ** Gordon Pusch ** Bruce Parrello ** Rob Edwards ** Andrei Osterman ** Michael Fonstein ** Svetlana Gerdes ** Olga Zagnitko ** Olga Vassieva ** Yakov Kogan ** Irina Goltsman * [http://www.mcs.anl.gov Mathematics and Computer Science Department] [http://www.anl.gov Argonne National Labs] ** Rick Stevens ** Terry Disz ** Robert Olson ** Folker Meyer ** Elizabeth Glass ** Chris Henry * [http://www.ci.uchicago.ed Computation Institute] [http://www.uchicago.edu University of Chicago] ** Daniela Bartels ** Matt Cohoon ** Michael Kubal ** William Mihalo ** Tobias Paczian ** Andreas Wilke ** Jen Zinner ** Alex Rodriguez ** Mark D'Souza ** Jared Wilkening * [http://www.uiuc.edu University of Illinois at Urbana-Champaign] ** Gary J. Olson ** Leslie McNeil * [http://www.hope.edu Hope College] ** Matt DeJongh ** Aaron Best * [http://www.utmem.edu/ University of Memphis Tennessee] ** Rami Aziz Alumni ** Daniel Paarmann 72e4901024b38a91976ab02866a6d6ad6e9490a8 2458 2457 2008-12-18T18:56:30Z Marland 16 wikitext text/x-wiki The people behind SEED are the following: * [http://www.thefig.info '''FIG'''] ** Ross Overbeek ** Veronika Vonstein ** Gordon Pusch ** Bruce Parrello ** Rob Edwards ** Andrei Osterman ** Michael Fonstein ** Svetlana Gerdes ** Olga Zagnitko ** Olga Vassieva ** Yakov Kogan ** Irina Goltsman * [http://www.mcs.anl.gov '''Mathematics and Computer Science Department'''] [http://www.anl.gov '''Argonne National Labs'''] ** Rick Stevens ** Terry Disz ** Robert Olson ** Folker Meyer ** Elizabeth Glass ** Chris Henry * [http://www.ci.uchicago.ed '''Computation Institute'''] [http://www.uchicago.edu '''University of Chicago'''] ** Daniela Bartels ** Matt Cohoon ** Michael Kubal ** William Mihalo ** Tobias Paczian ** Andreas Wilke ** Jen Zinner ** Alex Rodriguez ** Mark D'Souza ** Jared Wilkening * [http://www.uiuc.edu '''University of Illinois at Urbana-Champaign'''] ** Gary J. Olson ** Leslie McNeil * [http://www.hope.edu '''Hope College'''] ** Matt DeJongh ** Aaron Best * [http://www.utmem.edu/ '''University of Memphis Tennessee'''] ** Rami Aziz * '''Alumni''' ** Daniel Paarmann 55196bde248b5d73eaae29839f47c214c590fddb 2470 2458 2008-12-18T20:59:18Z Marland 16 wikitext text/x-wiki The people behind SEED are the following: * [http://www.thefig.info '''FIG'''] ** Ross Overbeek ** Veronika Vonstein ** Gordon Pusch ** Bruce Parrello ** Rob Edwards ** Andrei Osterman ** Michael Fonstein ** Svetlana Gerdes ** Olga Zagnitko ** Olga Vassieva ** Yakov Kogan ** Irina Goltsman * [http://www.mcs.anl.gov '''Mathematics and Computer Science Department'''] [http://www.anl.gov '''Argonne National Labs'''] ** Rick Stevens ** Terry Disz ** Robert Olson ** Folker Meyer ** Elizabeth Glass ** Chris Henry ** Jared Wilkening * [http://www.ci.uchicago.ed '''Computation Institute'''] [http://www.uchicago.edu '''University of Chicago'''] ** Daniela Bartels ** Michael Kubal ** William Mihalo ** Tobias Paczian ** Andreas Wilke ** Alex Rodriguez ** Mark D'Souza * [http://www.uiuc.edu '''University of Illinois at Urbana-Champaign'''] ** Gary J. Olson ** Leslie McNeil ** Claudia Reich * [http://www.hope.edu '''Hope College'''] ** Matt DeJongh ** Aaron Best * [http://www.utmem.edu/ '''University of Memphis Tennessee'''] ** Rami Aziz * '''Alumni''' ** Daniel Paarmann ** Jen Zinner ** Matt Cohoon 679ae2de2acbf14cdc576822f9597b9c8912b541 2473 2470 2009-01-08T18:14:30Z LeslieMcNeil 7 wikitext text/x-wiki The people behind SEED are the following: * [http://www.thefig.info '''FIG'''] ** Ross Overbeek ** Veronika Vonstein ** Gordon Pusch ** Bruce Parrello ** Rob Edwards ** Andrei Osterman ** Michael Fonstein ** Svetlana Gerdes ** Olga Zagnitko ** Olga Vassieva ** Yakov Kogan ** Irina Goltsman * [http://www.mcs.anl.gov '''Mathematics and Computer Science Department'''] [http://www.anl.gov '''Argonne National Labs'''] ** Rick Stevens ** Terry Disz ** Robert Olson ** Folker Meyer ** Elizabeth Glass ** Chris Henry ** Jared Wilkening * [http://www.ci.uchicago.ed '''Computation Institute'''] [http://www.uchicago.edu '''University of Chicago'''] ** Daniela Bartels ** Michael Kubal ** William Mihalo ** Tobias Paczian ** Andreas Wilke ** Alex Rodriguez ** Mark D'Souza * [http://www.uiuc.edu '''University of Illinois at Urbana-Champaign'''] ** Gary J. Olsen ** Leslie McNeil ** Claudia Reich * [http://www.hope.edu '''Hope College'''] ** Matt DeJongh ** Aaron Best * [http://www.utmem.edu/ '''University of Memphis Tennessee'''] ** Rami Aziz * '''Alumni''' ** Daniel Paarmann ** Jen Zinner ** Matt Cohoon cd1ae09a8bb814981595513048e3ee71b4e68cc4 2474 2473 2009-01-08T18:15:34Z LeslieMcNeil 7 wikitext text/x-wiki The people behind SEED are the following: * [http://www.thefig.info '''FIG'''] ** Ross Overbeek ** Veronika Vonstein ** Gordon Pusch ** Bruce Parrello ** Rob Edwards ** Andrei Osterman ** Michael Fonstein ** Svetlana Gerdes ** Olga Zagnitko ** Olga Vassieva ** Yakov Kogan ** Irina Goltsman * [http://www.mcs.anl.gov '''Mathematics and Computer Science Department'''] [http://www.anl.gov '''Argonne National Labs'''] ** Rick Stevens ** Terry Disz ** Robert Olson ** Folker Meyer ** Elizabeth Glass ** Chris Henry ** Jared Wilkening * [http://www.ci.uchicago.ed '''Computation Institute'''] [http://www.uchicago.edu '''University of Chicago'''] ** Daniela Bartels ** Michael Kubal ** William Mihalo ** Tobias Paczian ** Andreas Wilke ** Alex Rodriguez ** Mark D'Souza * [http://www.uiuc.edu '''University of Illinois at Urbana-Champaign'''] ** Gary J. Olsen ** Leslie McNeil ** Claudia Reich * [http://www.hope.edu '''Hope College'''] ** Matt DeJongh ** Aaron Best * [http://www.utmem.edu/ '''University of Tennessee Memphis Health Sciences Center'''] ** Rami Aziz * '''Alumni''' ** Daniel Paarmann ** Jen Zinner ** Matt Cohoon 00cb72f8bd74f2ec287978b13cc6508adc3aaed7 2475 2474 2009-01-08T20:14:14Z LeslieMcNeil 7 wikitext text/x-wiki The people behind SEED are the following: * [http://www.thefig.info '''FIG'''] ** Ross Overbeek ** Veronika Vonstein ** Gordon Pusch ** Bruce Parrello ** Rob Edwards ** Andrei Osterman ** Michael Fonstein ** Svetlana Gerdes ** Olga Zagnitko ** Olga Vassieva ** Yakov Kogan ** Irina Goltsman * [http://www.mcs.anl.gov '''Mathematics and Computer Science Department'''] [http://www.anl.gov '''Argonne National Labs'''] ** Rick Stevens ** Terry Disz ** Robert Olson ** Folker Meyer ** Elizabeth Glass ** Chris Henry ** Jared Wilkening * [http://www.ci.uchicago.ed '''Computation Institute'''] [http://www.uchicago.edu '''University of Chicago'''] ** Daniela Bartels ** Michael Kubal ** William Mihalo ** Tobias Paczian ** Andreas Wilke ** Alex Rodriguez ** Mark D'Souza ** Rami Aziz * [http://www.uiuc.edu '''University of Illinois at Urbana-Champaign'''] ** Gary J. Olsen ** Leslie McNeil ** Claudia Reich * [http://www.hope.edu '''Hope College'''] ** Matt DeJongh ** Aaron Best * '''Alumni''' ** Daniel Paarmann ** Jen Zinner ** Matt Cohoon e7994fd37d4187c3d7fa61807e6196b9b29b93f5 2479 2475 2009-01-14T23:39:14Z LeslieMcNeil 7 wikitext text/x-wiki The people behind SEED are the following: * [http://www.thefig.info '''FIG'''] ** Ross Overbeek ** Veronika Vonstein ** Gordon Pusch ** Bruce Parrello ** Rob Edwards ** Andrei Osterman ** Michael Fonstein ** Svetlana Gerdes ** Olga Zagnitko ** Olga Vassieva ** Yakov Kogan ** Irina Goltsman * [http://www.mcs.anl.gov '''Mathematics and Computer Science Department'''] [http://www.anl.gov '''Argonne National Labs'''] ** Rick Stevens ** Terry Disz ** Robert Olson ** Folker Meyer ** Elizabeth Glass ** Chris Henry ** Jared Wilkening * [http://www.ci.uchicago.edu '''Computation Institute'''] [http://www.uchicago.edu '''University of Chicago'''] ** Daniela Bartels ** Michael Kubal ** William Mihalo ** Tobias Paczian ** Andreas Wilke ** Alex Rodriguez ** Mark D'Souza ** Rami Aziz * [http://www.uiuc.edu '''University of Illinois at Urbana-Champaign'''] ** Gary J. Olsen ** Leslie McNeil ** Claudia Reich * [http://www.hope.edu '''Hope College'''] ** Matt DeJongh ** Aaron Best * '''Alumni''' ** Daniel Paarmann ** Jen Zinner ** Matt Cohoon 80ca3e439cc80bc46758bcb2082a0be2ce9f5447 0 1421 2459 1665 2008-12-18T18:59:53Z Marland 16 wikitext text/x-wiki '''RAST Sever Video Tutorials''' Coming soon ... 7fef8db6a6da3ddbc1c48ee4b4ab2265ee1731ae 0 1 2460 1792 2008-12-18T20:06:01Z LeslieMcNeil 7 wikitext text/x-wiki With the growing number of available genomes, the need for an environment to support effective comparative analysis increases. The original SEED Project was started in 2003 by the [http://thefig.info Fellowship for Interpretation of Genomes (FIG)] as a largely unfunded open source effort. Argonne National Laboratory and the University of Chicago joined the project, and now much of the activity occurs at those two institutions (as well as the University of Illinois at Urbana-Champaign, Hope college, San Diego State University, the Burnham Institute and a number of other institutions). The cooperative effort focuses on the development of the comparative genomics environment called the SEED and, more importantly, on the development of curated genomic data. [[Image:Data_lifecycle3.png|frame|thumbnail|50px|Flow of data in the SEED.]] Curation of genomic data ([[Glossary#Annotation|annotation]]) is done via the curation of [[Glossary#Subsystem|subsystems]] by an expert annotator across many genomes, not one a gene by gene basis. This is also detailed in our [[Annotating_1000_genomes|manifesto]]. From the curated subsystems we extract a set of freely available protein families ([[Glossary#FIGfam|FIGfams]]). These FIGfams form the core component of our RAST automated annotation technology. Answering numerous requests for automatic Seed-Quality annotations for more or less complete bacterial and archaeal genomes, we have established the free [http://rast.nmpdr.org RAST-Server] (RAST=Rapid Annotation using Subsytems Technology). Using similar technology, we make the [http://metagenomics.nmpdr.org Metagenomics-RAST-Server] freely available. We also provide a [http://seed-viewer.theseed.org/ SEED-Viewer] that allows read-only access to the latest curated data sets. For users interested in editing and learning how to use the system, we provide the [http://theseed.uchicago.edu/FIG/index.cgi Trial-SEED]. We make all our software and data available for download via [ftp://ftp.theseed.org], also see our [[DownloadPage]] page. * We request that groups using the SEED cite: Overbeek et al., [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16214803&query_hl=2&itool=pubmed_docsum|Nucleic Nucleic Acids Res 33(17)], 2005 ([http://www.theseed.org/SubsystemPaperSupplementalMaterial/index.html Supplementary material]) * We request that groups using the RAST server cite: Aziz et al., [http://www.ncbi.nlm.nih.gov/pubmed/18261238?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum| BMC Genomics], 2008 ([http://www.theseed.org/RASTPaperSupplementalMaterial/index.html Supplementary material]) * Our approaches to annotation, gene calling etc are outlined in a series of [[SOPs|Standard Operating Procedures]]. * Other [http://www.nmpdr.org/FIG/wiki/view.cgi/Main/Publications] 5127218b974ce70f0e57bf6f62d4e153651b4110 2461 2460 2008-12-18T20:08:11Z LeslieMcNeil 7 wikitext text/x-wiki With the growing number of available genomes, the need for an environment to support effective comparative analysis increases. The original SEED Project was started in 2003 by the [http://thefig.info Fellowship for Interpretation of Genomes (FIG)] as a largely unfunded open source effort. Argonne National Laboratory and the University of Chicago joined the project, and now much of the activity occurs at those two institutions (as well as the University of Illinois at Urbana-Champaign, Hope college, San Diego State University, the Burnham Institute and a number of other institutions). The cooperative effort focuses on the development of the comparative genomics environment called the SEED and, more importantly, on the development of curated genomic data. [[Image:Data_lifecycle3.png|frame|thumbnail|50px|Flow of data in the SEED.]] Curation of genomic data ([[Glossary#Annotation|annotation]]) is done via the curation of [[Glossary#Subsystem|subsystems]] by an expert annotator across many genomes, not one a gene by gene basis. This is also detailed in our [[Annotating_1000_genomes|manifesto]]. From the curated subsystems we extract a set of freely available protein families ([[Glossary#FIGfam|FIGfams]]). These FIGfams form the core component of our RAST automated annotation technology. Answering numerous requests for automatic Seed-Quality annotations for more or less complete bacterial and archaeal genomes, we have established the free [http://rast.nmpdr.org RAST-Server] (RAST=Rapid Annotation using Subsytems Technology). Using similar technology, we make the [http://metagenomics.nmpdr.org Metagenomics-RAST-Server] freely available. We also provide a [http://seed-viewer.theseed.org/ SEED-Viewer] that allows read-only access to the latest curated data sets. For users interested in editing and learning how to use the system, we provide the [http://theseed.uchicago.edu/FIG/index.cgi Trial-SEED]. We make all our software and data available for download via [ftp://ftp.theseed.org], also see our [[DownloadPage]] page. * We request that groups using the SEED cite: Overbeek et al., [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16214803&query_hl=2&itool=pubmed_docsum|Nucleic Nucleic Acids Res 33(17)], 2005 ([http://www.theseed.org/SubsystemPaperSupplementalMaterial/index.html Supplementary material]) * We request that groups using the RAST server cite: Aziz et al., [http://www.ncbi.nlm.nih.gov/pubmed/18261238?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum| BMC Genomics], 2008 ([http://www.theseed.org/RASTPaperSupplementalMaterial/index.html Supplementary material]) * Our approaches to annotation, gene calling etc are outlined in a series of [[SOPs|Standard Operating Procedures]]. * Read about how other groups have used our tools in their research on our [http://www.nmpdr.org/FIG/wiki/view.cgi/Main/Publications|Publications] page. 65b1a05c1ee87427b621ff30fd8560954aa1b012 2462 2461 2008-12-18T20:09:18Z LeslieMcNeil 7 wikitext text/x-wiki With the growing number of available genomes, the need for an environment to support effective comparative analysis increases. The original SEED Project was started in 2003 by the [http://thefig.info Fellowship for Interpretation of Genomes (FIG)] as a largely unfunded open source effort. Argonne National Laboratory and the University of Chicago joined the project, and now much of the activity occurs at those two institutions (as well as the University of Illinois at Urbana-Champaign, Hope college, San Diego State University, the Burnham Institute and a number of other institutions). The cooperative effort focuses on the development of the comparative genomics environment called the SEED and, more importantly, on the development of curated genomic data. [[Image:Data_lifecycle3.png|frame|thumbnail|50px|Flow of data in the SEED.]] Curation of genomic data ([[Glossary#Annotation|annotation]]) is done via the curation of [[Glossary#Subsystem|subsystems]] by an expert annotator across many genomes, not one a gene by gene basis. This is also detailed in our [[Annotating_1000_genomes|manifesto]]. From the curated subsystems we extract a set of freely available protein families ([[Glossary#FIGfam|FIGfams]]). These FIGfams form the core component of our RAST automated annotation technology. Answering numerous requests for automatic Seed-Quality annotations for more or less complete bacterial and archaeal genomes, we have established the free [http://rast.nmpdr.org RAST-Server] (RAST=Rapid Annotation using Subsytems Technology). Using similar technology, we make the [http://metagenomics.nmpdr.org Metagenomics-RAST-Server] freely available. We also provide a [http://seed-viewer.theseed.org/ SEED-Viewer] that allows read-only access to the latest curated data sets. For users interested in editing and learning how to use the system, we provide the [http://theseed.uchicago.edu/FIG/index.cgi Trial-SEED]. We make all our software and data available for download via [ftp://ftp.theseed.org], also see our [[DownloadPage]] page. * We request that groups using the SEED cite: Overbeek et al., [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16214803&query_hl=2&itool=pubmed_docsum|Nucleic Nucleic Acids Res 33(17)], 2005 ([http://www.theseed.org/SubsystemPaperSupplementalMaterial/index.html Supplementary material]) * We request that groups using the RAST server cite: Aziz et al., [http://www.ncbi.nlm.nih.gov/pubmed/18261238?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum| BMC Genomics], 2008 ([http://www.theseed.org/RASTPaperSupplementalMaterial/index.html Supplementary material]) * Our approaches to annotation, gene calling etc are outlined in a series of [[SOPs|Standard Operating Procedures]]. * Read about how other groups have used our tools in their research on our [[http://www.nmpdr.org/FIG/wiki/view.cgi/Main/Publications| Publications]] page. 45cb1ba080e6a71ee184bf86cec25f21deaf20dd 2463 2462 2008-12-18T20:18:58Z LeslieMcNeil 7 wikitext text/x-wiki With the growing number of available genomes, the need for an environment to support effective comparative analysis increases. The original SEED Project was started in 2003 by the [http://thefig.info Fellowship for Interpretation of Genomes (FIG)] as a largely unfunded open source effort. Argonne National Laboratory and the University of Chicago joined the project, and now much of the activity occurs at those two institutions (as well as the University of Illinois at Urbana-Champaign, Hope college, San Diego State University, the Burnham Institute and a number of other institutions). The cooperative effort focuses on the development of the comparative genomics environment called the SEED and, more importantly, on the development of curated genomic data. [[Image:Data_lifecycle3.png|frame|thumbnail|50px|Flow of data in the SEED.]] Curation of genomic data ([[Glossary#Annotation|annotation]]) is done via the curation of [[Glossary#Subsystem|subsystems]] by an expert annotator across many genomes, not one a gene by gene basis. This is also detailed in our [[Annotating_1000_genomes|manifesto]]. From the curated subsystems we extract a set of freely available protein families ([[Glossary#FIGfam|FIGfams]]). These FIGfams form the core component of our RAST automated annotation technology. Answering numerous requests for automatic Seed-Quality annotations for more or less complete bacterial and archaeal genomes, we have established the free [http://rast.nmpdr.org RAST-Server] (RAST=Rapid Annotation using Subsytems Technology). Using similar technology, we make the [http://metagenomics.nmpdr.org Metagenomics-RAST-Server] freely available. We also provide a [http://seed-viewer.theseed.org/ SEED-Viewer] that allows read-only access to the latest curated data sets. For users interested in editing and learning how to use the system, we provide the [http://theseed.uchicago.edu/FIG/index.cgi Trial-SEED]. We make all our software and data available for download via [ftp://ftp.theseed.org], also see our [[DownloadPage]] page. * We request that groups using the SEED cite: Overbeek et al., [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16214803&query_hl=2&itool=pubmed_docsum|Nucleic Nucleic Acids Res 33(17)], 2005 ([http://www.theseed.org/SubsystemPaperSupplementalMaterial/index.html Supplementary material]) * We request that groups using the RAST server cite: Aziz et al., [http://www.ncbi.nlm.nih.gov/pubmed/18261238?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum| BMC Genomics], 2008 ([http://www.theseed.org/RASTPaperSupplementalMaterial/index.html Supplementary material]) * Our approaches to annotation, gene calling, etc. are outlined in a series of [[SOPs|Standard Operating Procedures]]. * Read about how other groups have used our tools in their research on our [http://www.nmpdr.org/FIG/wiki/view.cgi/Main/Publications| Publications] page. 94957e8694cdd4e654e1a8b57239ab3f234528f0 2464 2463 2008-12-18T20:21:59Z LeslieMcNeil 7 wikitext text/x-wiki With the growing number of available genomes, the need for an environment to support effective comparative analysis increases. The original SEED Project was started in 2003 by the [http://thefig.info Fellowship for Interpretation of Genomes (FIG)] as a largely unfunded open source effort. Argonne National Laboratory and the University of Chicago joined the project, and now much of the activity occurs at those two institutions (as well as the University of Illinois at Urbana-Champaign, Hope college, San Diego State University, the Burnham Institute and a number of other institutions). The cooperative effort focuses on the development of the comparative genomics environment called the SEED and, more importantly, on the development of curated genomic data. [[Image:Data_lifecycle3.png|frame|thumbnail|50px|Flow of data in the SEED.]] Curation of genomic data ([[Glossary#Annotation|annotation]]) is done via the curation of [[Glossary#Subsystem|subsystems]] by an expert annotator across many genomes, not one a gene by gene basis. This is also detailed in our [[Annotating_1000_genomes|manifesto]]. From the curated subsystems we extract a set of freely available protein families ([[Glossary#FIGfam|FIGfams]]). These FIGfams form the core component of our RAST automated annotation technology. Answering numerous requests for automatic Seed-Quality annotations for more or less complete bacterial and archaeal genomes, we have established the free [http://rast.nmpdr.org RAST-Server] (RAST=Rapid Annotation using Subsytems Technology). Using similar technology, we make the [http://metagenomics.nmpdr.org Metagenomics-RAST-Server] freely available. We also provide a [http://seed-viewer.theseed.org/ SEED-Viewer] that allows read-only access to the latest curated data sets. For users interested in editing and learning how to use the system, we provide the [http://theseed.uchicago.edu/FIG/index.cgi Trial-SEED]. We make all our software and data available for download via [ftp://ftp.theseed.org], also see our [[DownloadPage]] page. * We request that groups using the SEED cite: Overbeek et al., [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16214803&query_hl=2&itool=pubmed_docsum|Nucleic Nucleic Acids Res 33(17)], 2005 ([http://www.theseed.org/SubsystemPaperSupplementalMaterial/index.html Supplementary material]) * We request that groups using the RAST server cite: Aziz et al., [http://www.ncbi.nlm.nih.gov/pubmed/18261238?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum| BMC Genomics], 2008 ([http://www.theseed.org/RASTPaperSupplementalMaterial/index.html Supplementary material]) * Our approaches to annotation, gene calling, etc. are outlined in a series of [http://www.nmpdr.org/FIG/wiki/view.cgi/SOP/WebHome|Standard Operating Procedures]. * Read about how other groups have used our tools in their research on our [http://www.nmpdr.org/FIG/wiki/view.cgi/Main/Publications| Publications] page. ae9b23a7c806a4e887b3dc1bb30aa8996a8a71aa 2465 2464 2008-12-18T20:22:21Z LeslieMcNeil 7 wikitext text/x-wiki With the growing number of available genomes, the need for an environment to support effective comparative analysis increases. The original SEED Project was started in 2003 by the [http://thefig.info Fellowship for Interpretation of Genomes (FIG)] as a largely unfunded open source effort. Argonne National Laboratory and the University of Chicago joined the project, and now much of the activity occurs at those two institutions (as well as the University of Illinois at Urbana-Champaign, Hope college, San Diego State University, the Burnham Institute and a number of other institutions). The cooperative effort focuses on the development of the comparative genomics environment called the SEED and, more importantly, on the development of curated genomic data. [[Image:Data_lifecycle3.png|frame|thumbnail|50px|Flow of data in the SEED.]] Curation of genomic data ([[Glossary#Annotation|annotation]]) is done via the curation of [[Glossary#Subsystem|subsystems]] by an expert annotator across many genomes, not one a gene by gene basis. This is also detailed in our [[Annotating_1000_genomes|manifesto]]. From the curated subsystems we extract a set of freely available protein families ([[Glossary#FIGfam|FIGfams]]). These FIGfams form the core component of our RAST automated annotation technology. Answering numerous requests for automatic Seed-Quality annotations for more or less complete bacterial and archaeal genomes, we have established the free [http://rast.nmpdr.org RAST-Server] (RAST=Rapid Annotation using Subsytems Technology). Using similar technology, we make the [http://metagenomics.nmpdr.org Metagenomics-RAST-Server] freely available. We also provide a [http://seed-viewer.theseed.org/ SEED-Viewer] that allows read-only access to the latest curated data sets. For users interested in editing and learning how to use the system, we provide the [http://theseed.uchicago.edu/FIG/index.cgi Trial-SEED]. We make all our software and data available for download via [ftp://ftp.theseed.org], also see our [[DownloadPage]] page. * We request that groups using the SEED cite: Overbeek et al., [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16214803&query_hl=2&itool=pubmed_docsum|Nucleic Nucleic Acids Res 33(17)], 2005 ([http://www.theseed.org/SubsystemPaperSupplementalMaterial/index.html Supplementary material]) * We request that groups using the RAST server cite: Aziz et al., [http://www.ncbi.nlm.nih.gov/pubmed/18261238?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum| BMC Genomics], 2008 ([http://www.theseed.org/RASTPaperSupplementalMaterial/index.html Supplementary material]) * Our approaches to annotation, gene calling, etc. are outlined in a series of [http://www.nmpdr.org/FIG/wiki/view.cgi/SOP/WebHome| Standard Operating Procedures]. * Read about how other groups have used our tools in their research on our [http://www.nmpdr.org/FIG/wiki/view.cgi/Main/Publications| Publications] page. 7110cfd766c614a17d6b5c29e8653b1f48b3d9c7 2466 2465 2008-12-18T20:25:29Z LeslieMcNeil 7 wikitext text/x-wiki With the growing number of available genomes, the need for an environment to support effective comparative analysis increases. The original SEED Project was started in 2003 by the [http://thefig.info Fellowship for Interpretation of Genomes (FIG)] as a largely unfunded open source effort. Argonne National Laboratory and the University of Chicago joined the project, and now much of the activity occurs at those two institutions (as well as the University of Illinois at Urbana-Champaign, Hope college, San Diego State University, the Burnham Institute and a number of other institutions). The cooperative effort focuses on the development of the comparative genomics environment called the SEED and, more importantly, on the development of curated genomic data. [[Image:Data_lifecycle3.png|frame|thumbnail|50px|Flow of data in the SEED.]] Curation of genomic data ([[Glossary#Annotation|annotation]]) is done via the curation of [[Glossary#Subsystem|subsystems]] by an expert annotator across many genomes, not one a gene by gene basis. This is also detailed in our [[Annotating_1000_genomes|manifesto]]. From the curated subsystems we extract a set of freely available protein families ([[Glossary#FIGfam|FIGfams]]). These FIGfams form the core component of our RAST automated annotation technology. Answering numerous requests for automatic Seed-Quality annotations for more or less complete bacterial and archaeal genomes, we have established the free [http://rast.nmpdr.org RAST-Server] (RAST=Rapid Annotation using Subsytems Technology). Using similar technology, we make the [http://metagenomics.nmpdr.org Metagenomics-RAST-Server] freely available. We also provide a [http://seed-viewer.theseed.org/ SEED-Viewer] that allows read-only access to the latest curated data sets. For users interested in editing and learning how to use the system, we provide the [http://theseed.uchicago.edu/FIG/index.cgi Trial-SEED]. We make all our software and data available for download via [ftp://ftp.theseed.org], also see our [[DownloadPage]] page. * We request that groups using the SEED cite: Overbeek et al., [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16214803&query_hl=2&itool=pubmed_docsum|Nucleic Nucleic Acids Res 33(17)], 2005 ([http://www.theseed.org/SubsystemPaperSupplementalMaterial/index.html Supplementary material]) * We request that groups using the RAST server cite: Aziz et al., [http://www.ncbi.nlm.nih.gov/pubmed/18261238?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum| BMC Genomics], 2008 ([http://www.theseed.org/RASTPaperSupplementalMaterial/index.html Supplementary material]) * Our approaches to annotation, gene calling, etc. are outlined in a series of [http://www.nmpdr.org/FIG/wiki/view.cgi/SOP/WebHome| Standard Operating Procedures]. * Read about how other groups have used our tools in their research on our [http://www.nmpdr.org/FIG/wiki/view.cgi/Main/Publications#Using%20our%20tools| Publications] page. 0686d15f77bebc3f4cd815763745644fde4c31e5 2467 2466 2008-12-18T20:26:30Z LeslieMcNeil 7 wikitext text/x-wiki With the growing number of available genomes, the need for an environment to support effective comparative analysis increases. The original SEED Project was started in 2003 by the [http://thefig.info Fellowship for Interpretation of Genomes (FIG)] as a largely unfunded open source effort. Argonne National Laboratory and the University of Chicago joined the project, and now much of the activity occurs at those two institutions (as well as the University of Illinois at Urbana-Champaign, Hope college, San Diego State University, the Burnham Institute and a number of other institutions). The cooperative effort focuses on the development of the comparative genomics environment called the SEED and, more importantly, on the development of curated genomic data. [[Image:Data_lifecycle3.png|frame|thumbnail|50px|Flow of data in the SEED.]] Curation of genomic data ([[Glossary#Annotation|annotation]]) is done via the curation of [[Glossary#Subsystem|subsystems]] by an expert annotator across many genomes, not one a gene by gene basis. This is also detailed in our [[Annotating_1000_genomes|manifesto]]. From the curated subsystems we extract a set of freely available protein families ([[Glossary#FIGfam|FIGfams]]). These FIGfams form the core component of our RAST automated annotation technology. Answering numerous requests for automatic Seed-Quality annotations for more or less complete bacterial and archaeal genomes, we have established the free [http://rast.nmpdr.org RAST-Server] (RAST=Rapid Annotation using Subsytems Technology). Using similar technology, we make the [http://metagenomics.nmpdr.org Metagenomics-RAST-Server] freely available. We also provide a [http://seed-viewer.theseed.org/ SEED-Viewer] that allows read-only access to the latest curated data sets. For users interested in editing and learning how to use the system, we provide the [http://theseed.uchicago.edu/FIG/index.cgi Trial-SEED]. We make all our software and data available for download via [ftp://ftp.theseed.org], also see our [[DownloadPage]] page. * We request that groups using the SEED cite: Overbeek et al., [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16214803&query_hl=2&itool=pubmed_docsum|Nucleic Nucleic Acids Res 33(17)], 2005 ([http://www.theseed.org/SubsystemPaperSupplementalMaterial/index.html Supplementary material]) * We request that groups using the RAST server cite: Aziz et al., [http://www.ncbi.nlm.nih.gov/pubmed/18261238?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum| BMC Genomics], 2008 ([http://www.theseed.org/RASTPaperSupplementalMaterial/index.html Supplementary material]) * Our approaches to annotation, gene calling, etc. are outlined in a series of [http://www.nmpdr.org/FIG/wiki/view.cgi/SOP/WebHome| Standard Operating Procedures]. * Read about how other groups have used our tools in their research on our [http://www.nmpdr.org/FIG/wiki/view.cgi/Main/Publications#Using| Publications] page. 851d46bf1100fb1ad2fd2ffd9b7e87c858418da0 2468 2467 2008-12-18T20:29:44Z LeslieMcNeil 7 wikitext text/x-wiki With the growing number of available genomes, the need for an environment to support effective comparative analysis increases. The original SEED Project was started in 2003 by the [http://thefig.info Fellowship for Interpretation of Genomes (FIG)] as a largely unfunded open source effort. Argonne National Laboratory and the University of Chicago joined the project, and now much of the activity occurs at those two institutions (as well as the University of Illinois at Urbana-Champaign, Hope college, San Diego State University, the Burnham Institute and a number of other institutions). The cooperative effort focuses on the development of the comparative genomics environment called the SEED and, more importantly, on the development of curated genomic data. [[Image:Data_lifecycle3.png|frame|thumbnail|50px|Flow of data in the SEED.]] Curation of genomic data ([[Glossary#Annotation|annotation]]) is done via the curation of [[Glossary#Subsystem|subsystems]] by an expert annotator across many genomes, not one a gene by gene basis. This is also detailed in our [[Annotating_1000_genomes|manifesto]]. From the curated subsystems we extract a set of freely available protein families ([[Glossary#FIGfam|FIGfams]]). These FIGfams form the core component of our RAST automated annotation technology. Answering numerous requests for automatic Seed-Quality annotations for more or less complete bacterial and archaeal genomes, we have established the free [http://rast.nmpdr.org RAST-Server] (RAST=Rapid Annotation using Subsytems Technology). Using similar technology, we make the [http://metagenomics.nmpdr.org Metagenomics-RAST-Server] freely available. We also provide a [http://seed-viewer.theseed.org/ SEED-Viewer] that allows read-only access to the latest curated data sets. For users interested in editing and learning how to use the system, we provide the [http://theseed.uchicago.edu/FIG/index.cgi Trial-SEED]. We make all our software and data available for download via [ftp://ftp.theseed.org], also see our [[DownloadPage]] page. * We request that groups using the SEED cite: Overbeek et al., [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16214803&query_hl=2&itool=pubmed_docsum|Nucleic Nucleic Acids Res 33(17)], 2005 ([http://www.theseed.org/SubsystemPaperSupplementalMaterial/index.html Supplementary material]) * We request that groups using the RAST server cite: Aziz et al., [http://www.ncbi.nlm.nih.gov/pubmed/18261238?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum| BMC Genomics], 2008 ([http://www.theseed.org/RASTPaperSupplementalMaterial/index.html Supplementary material]) * Our approaches to annotation, gene calling, etc. are outlined in a series of [http://www.nmpdr.org/FIG/wiki/view.cgi/SOP/WebHome| Standard Operating Procedures]. * Read about how other groups have used our tools in their research on our [http://www.nmpdr.org/FIG/wiki/view.cgi/Main/Publications#Using | Publications] page. 81de7ad0f142c0a2d7834b3137f39192d35f93cc 2469 2468 2008-12-18T20:31:31Z LeslieMcNeil 7 wikitext text/x-wiki With the growing number of available genomes, the need for an environment to support effective comparative analysis increases. The original SEED Project was started in 2003 by the [http://thefig.info Fellowship for Interpretation of Genomes (FIG)] as a largely unfunded open source effort. Argonne National Laboratory and the University of Chicago joined the project, and now much of the activity occurs at those two institutions (as well as the University of Illinois at Urbana-Champaign, Hope college, San Diego State University, the Burnham Institute and a number of other institutions). The cooperative effort focuses on the development of the comparative genomics environment called the SEED and, more importantly, on the development of curated genomic data. [[Image:Data_lifecycle3.png|frame|thumbnail|50px|Flow of data in the SEED.]] Curation of genomic data ([[Glossary#Annotation|annotation]]) is done via the curation of [[Glossary#Subsystem|subsystems]] by an expert annotator across many genomes, not one a gene by gene basis. This is also detailed in our [[Annotating_1000_genomes|manifesto]]. From the curated subsystems we extract a set of freely available protein families ([[Glossary#FIGfam|FIGfams]]). These FIGfams form the core component of our RAST automated annotation technology. Answering numerous requests for automatic Seed-Quality annotations for more or less complete bacterial and archaeal genomes, we have established the free [http://rast.nmpdr.org RAST-Server] (RAST=Rapid Annotation using Subsytems Technology). Using similar technology, we make the [http://metagenomics.nmpdr.org Metagenomics-RAST-Server] freely available. We also provide a [http://seed-viewer.theseed.org/ SEED-Viewer] that allows read-only access to the latest curated data sets. For users interested in editing and learning how to use the system, we provide the [http://theseed.uchicago.edu/FIG/index.cgi Trial-SEED]. We make all our software and data available for download via [ftp://ftp.theseed.org], also see our [[DownloadPage]] page. * We request that groups using the SEED cite: Overbeek et al., [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16214803&query_hl=2&itool=pubmed_docsum|Nucleic Nucleic Acids Res 33(17)], 2005 ([http://www.theseed.org/SubsystemPaperSupplementalMaterial/index.html Supplementary material]) * We request that groups using the RAST server cite: Aziz et al., [http://www.ncbi.nlm.nih.gov/pubmed/18261238?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum| BMC Genomics], 2008 ([http://www.theseed.org/RASTPaperSupplementalMaterial/index.html Supplementary material]) * Our approaches to annotation, gene calling, etc. are outlined in a series of [http://www.nmpdr.org/FIG/wiki/view.cgi/SOP/WebHome| Standard Operating Procedures]. * Read about how other groups have used our tools in their research on our [http://www.nmpdr.org/FIG/wiki/view.cgi/Main/Publications#Using Publications] page. 61dff6e067503e2e0659a536eb24e11ec5e9cce6 2481 2469 2009-11-23T20:03:02Z FolkerMeyer 2 added link to FIGfam page wikitext text/x-wiki With the growing number of available genomes, the need for an environment to support effective comparative analysis increases. The original SEED Project was started in 2003 by the [http://thefig.info Fellowship for Interpretation of Genomes (FIG)] as a largely unfunded open source effort. Argonne National Laboratory and the University of Chicago joined the project, and now much of the activity occurs at those two institutions (as well as the University of Illinois at Urbana-Champaign, Hope college, San Diego State University, the Burnham Institute and a number of other institutions). The cooperative effort focuses on the development of the comparative genomics environment called the SEED and, more importantly, on the development of curated genomic data. [[Image:Data_lifecycle3.png|frame|thumbnail|50px|Flow of data in the SEED.]] Curation of genomic data ([[Glossary#Annotation|annotation]]) is done via the curation of [[Glossary#Subsystem|subsystems]] by an expert annotator across many genomes, not one a gene by gene basis. This is also detailed in our [[Annotating_1000_genomes|manifesto]]. From the curated subsystems we extract a set of freely available protein families ([http://seed-viewer.theseed.org/seedviewer.cgi?page=FigFamViewer FIGfams]). These FIGfams form the core component of our RAST automated annotation technology. Answering numerous requests for automatic Seed-Quality annotations for more or less complete bacterial and archaeal genomes, we have established the free [http://rast.nmpdr.org RAST-Server] (RAST=Rapid Annotation using Subsytems Technology). Using similar technology, we make the [http://metagenomics.nmpdr.org Metagenomics-RAST-Server] freely available. We also provide a [http://seed-viewer.theseed.org/ SEED-Viewer] that allows read-only access to the latest curated data sets. For users interested in editing and learning how to use the system, we provide the [http://theseed.uchicago.edu/FIG/index.cgi Trial-SEED]. We make all our software and data available for download via [ftp://ftp.theseed.org], also see our [[DownloadPage]] page. * We request that groups using the SEED cite: Overbeek et al., [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16214803&query_hl=2&itool=pubmed_docsum|Nucleic Nucleic Acids Res 33(17)], 2005 ([http://www.theseed.org/SubsystemPaperSupplementalMaterial/index.html Supplementary material]) * We request that groups using the RAST server cite: Aziz et al., [http://www.ncbi.nlm.nih.gov/pubmed/18261238?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum| BMC Genomics], 2008 ([http://www.theseed.org/RASTPaperSupplementalMaterial/index.html Supplementary material]) * Our approaches to annotation, gene calling, etc. are outlined in a series of [http://www.nmpdr.org/FIG/wiki/view.cgi/SOP/WebHome| Standard Operating Procedures]. * Read about how other groups have used our tools in their research on our [http://www.nmpdr.org/FIG/wiki/view.cgi/Main/Publications#Using Publications] page. 2521f9b133591b7f89aa3d6f3b34e18916ab0cdd 2485 2481 2010-06-11T20:52:03Z TerryDisz 4 wikitext text/x-wiki With the growing number of available genomes, the need for an environment to support effective comparative analysis increases. The original SEED Project was started in 2003 by the [http://thefig.info Fellowship for Interpretation of Genomes (FIG)] as a largely unfunded open source effort. Argonne National Laboratory and the University of Chicago joined the project, and now much of the activity occurs at those two institutions (as well as the University of Illinois at Urbana-Champaign, Hope college, San Diego State University, the Burnham Institute and a number of other institutions). The cooperative effort focuses on the development of the comparative genomics environment called the SEED and, more importantly, on the development of curated genomic data. [[Image:Data_lifecycle3.png|frame|thumbnail|50px|Flow of data in the SEED.]] Curation of genomic data ([[Glossary#Annotation|annotation]]) is done via the curation of [[Glossary#Subsystem|subsystems]] by an expert annotator across many genomes, not on a gene by gene basis. This is also detailed in our [[Annotating_1000_genomes|manifesto]]. From the curated subsystems we extract a set of freely available protein families ([http://seed-viewer.theseed.org/seedviewer.cgi?page=FigFamViewer FIGfams]). These FIGfams form the core component of our RAST automated annotation technology. Answering numerous requests for automatic Seed-Quality annotations for more or less complete bacterial and archaeal genomes, we have established the free [http://rast.nmpdr.org RAST-Server] (RAST=Rapid Annotation using Subsytems Technology). Using similar technology, we make the [http://metagenomics.nmpdr.org Metagenomics-RAST-Server] freely available. We also provide a [http://seed-viewer.theseed.org/ SEED-Viewer] that allows read-only access to the latest curated data sets. For users interested in editing and learning how to use the system, we provide the [http://theseed.uchicago.edu/FIG/index.cgi Trial-SEED]. We make all our software and data available for download via [ftp://ftp.theseed.org], also see our [[DownloadPage]] page. * We request that groups using the SEED cite: Overbeek et al., [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16214803&query_hl=2&itool=pubmed_docsum|Nucleic Nucleic Acids Res 33(17)], 2005 ([http://www.theseed.org/SubsystemPaperSupplementalMaterial/index.html Supplementary material]) * We request that groups using the RAST server cite: Aziz et al., [http://www.ncbi.nlm.nih.gov/pubmed/18261238?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum| BMC Genomics], 2008 ([http://www.theseed.org/RASTPaperSupplementalMaterial/index.html Supplementary material]) * Our approaches to annotation, gene calling, etc. are outlined in a series of [http://www.nmpdr.org/FIG/wiki/view.cgi/SOP/WebHome| Standard Operating Procedures]. * Read about how other groups have used our tools in their research on our [http://www.nmpdr.org/FIG/wiki/view.cgi/Main/Publications#Using Publications] page. 1d114e57bd2b6254050a670e545a2ee84b801620 8 1090 2471 1752 2009-01-06T14:01:24Z Marland 16 wikitext text/x-wiki * Navigation ** Home_of_the_SEED|Home of the SEED ** Annotating_1000_genomes|Manifesto ** SEED_People| SEED People ** Contact| Contact * SEEDs ** http://seed-viewer.theseed.org/|SEED-Viewer ** http://theseed.uchicago.edu/FIG/index.cgi|Public-SEED * Applications ** http://www.nmpdr.org/|NMPDR ** http://rast.nmpdr.org/|RAST Annotation Server ** http://metagenomics.nmpdr.org/|Metagenomics RAST Server * Documentation ** RAST_Tutorial|RAST Server Tutorial ** MG_RAST_Tutorial|MG-RAST Tutorial ** SEED_Viewer_Tutorial|SEED Viewer Tutorial * Miscellaneous ** DownloadPage|Download Page ** Glossary|FAQ Frequently Asked Questions ** Glossary|Glossary ** SOPs|SOPs ** SpecialPurposeDBs|Special Purpose DBs 552613f989153eda26ef1c8386e60b4b4544a3b8 2476 2471 2009-01-09T21:15:21Z LeslieMcNeil 7 wikitext text/x-wiki * Navigation ** Home_of_the_SEED|Home of the SEED ** Annotating_1000_genomes|Manifesto ** SEED_People| SEED People ** Contact| Contact * SEEDs ** http://seed-viewer.theseed.org/|SEED-Viewer ** http://theseed.uchicago.edu/FIG/index.cgi|Public-SEED * Applications ** http://www.nmpdr.org/|NMPDR ** http://rast.nmpdr.org/|RAST Annotation Server ** http://metagenomics.nmpdr.org/|Metagenomics RAST Server * Documentation ** http://www.nmpdr.org/FIG/wiki/view.cgi/Main/RAST |RAST Server Tutorial ** MG_RAST_Tutorial|MG-RAST Tutorial ** SEED_Viewer_Tutorial|SEED Viewer Tutorial * Miscellaneous ** DownloadPage|Download Page ** Glossary|FAQ Frequently Asked Questions ** Glossary|Glossary ** SOPs|SOPs ** SpecialPurposeDBs|Special Purpose DBs e073375e18bbe11242ec3ad9025847d42e1370bb 2477 2476 2009-01-10T23:23:44Z LeslieMcNeil 7 wikitext text/x-wiki * Navigation ** Home_of_the_SEED|Home of the SEED ** Annotating_1000_genomes|Manifesto ** SEED_People| SEED People ** Contact| Contact * SEEDs ** http://seed-viewer.theseed.org/|SEED-Viewer ** http://theseed.uchicago.edu/FIG/index.cgi|Public-SEED * Applications ** http://www.nmpdr.org/|NMPDR ** http://rast.nmpdr.org/|RAST Annotation Server ** http://metagenomics.nmpdr.org/|Metagenomics RAST Server * Documentation ** http://www.nmpdr.org/FIG/wiki/view.cgi/Main/RAST|RAST Server Tutorial ** http://www.nmpdr.org/FIG/wiki/view.cgi/Main/MG-RAST|MG-RAST Tutorial ** SEED_Viewer_Tutorial|SEED Viewer Tutorial * Miscellaneous ** DownloadPage|Download Page ** Glossary|FAQ Frequently Asked Questions ** Glossary|Glossary ** SOPs|SOPs ** SpecialPurposeDBs|Special Purpose DBs 142a527ddb9976476ed79621a9e41b68abd2342f 2478 2477 2009-01-10T23:27:27Z LeslieMcNeil 7 wikitext text/x-wiki * Navigation ** Home_of_the_SEED|Home of the SEED ** Annotating_1000_genomes|Manifesto ** SEED_People| SEED People ** Contact| Contact * SEEDs ** http://seed-viewer.theseed.org/|SEED-Viewer ** http://theseed.uchicago.edu/FIG/index.cgi|Public-SEED * Applications ** http://www.nmpdr.org/|NMPDR ** http://rast.nmpdr.org/|RAST Annotation Server ** http://metagenomics.nmpdr.org/|Metagenomics RAST Server * Documentation ** http://www.nmpdr.org/FIG/wiki/view.cgi/Main/RAST|RAST Server Tutorial ** http://www.nmpdr.org/FIG/wiki/view.cgi/Main/MG-RAST|MG-RAST Tutorial ** SEED_Viewer_Tutorial|SEED Viewer Tutorial * Miscellaneous ** DownloadPage|Download Page ** http://www.nmpdr.org/FIG/wiki/view.cgi/Main/FAQS|FAQ Frequently Asked Questions ** Glossary|Glossary ** SOPs|SOPs ** SpecialPurposeDBs|Special Purpose DBs ee867af0c8adac2c72e682420a6a949b1c0232f4 2482 2478 2009-12-16T18:07:34Z BruceParrello 19 wikitext text/x-wiki * Navigation ** Home_of_the_SEED|Home of the SEED ** Annotating_1000_genomes|Manifesto ** SEED_People| SEED People ** Contact| Contact * SEEDs ** http://seed-viewer.theseed.org/|SEED-Viewer ** http://theseed.uchicago.edu/FIG/index.cgi|Public-SEED * Applications ** http://servers.nmpdr.org/|SEED Servers ** http://rast.nmpdr.org/|RAST Annotation Server ** http://metagenomics.nmpdr.org/|Metagenomics RAST Server * Documentation ** http://www.nmpdr.org/FIG/wiki/view.cgi/Main/RAST|RAST Server Tutorial ** http://www.nmpdr.org/FIG/wiki/view.cgi/Main/MG-RAST|MG-RAST Tutorial ** SEED_Viewer_Tutorial|SEED Viewer Tutorial * Miscellaneous ** DownloadPage|Download Page ** http://www.nmpdr.org/FIG/wiki/view.cgi/Main/FAQS|FAQ Frequently Asked Questions ** Glossary|Glossary ** SOPs|SOPs ** SpecialPurposeDBs|Special Purpose DBs 565cb24b04a2e4c1e312259c92b8bff92d1cb512 2483 2482 2009-12-16T18:08:11Z BruceParrello 19 wikitext text/x-wiki * Navigation ** Home_of_the_SEED|Home of the SEED ** Annotating_1000_genomes|Manifesto ** SEED_People| SEED People ** Contact| Contact * SEEDs ** http://seed-viewer.theseed.org/|SEED-Viewer ** http://theseed.uchicago.edu/FIG/index.cgi|Public-SEED * Applications ** http://servers.nmpdr.org/|Network-Based SEED API ** http://rast.nmpdr.org/|RAST Annotation Server ** http://metagenomics.nmpdr.org/|Metagenomics RAST Server * Documentation ** http://www.nmpdr.org/FIG/wiki/view.cgi/Main/RAST|RAST Server Tutorial ** http://www.nmpdr.org/FIG/wiki/view.cgi/Main/MG-RAST|MG-RAST Tutorial ** SEED_Viewer_Tutorial|SEED Viewer Tutorial * Miscellaneous ** DownloadPage|Download Page ** http://www.nmpdr.org/FIG/wiki/view.cgi/Main/FAQS|FAQ Frequently Asked Questions ** Glossary|Glossary ** SOPs|SOPs ** SpecialPurposeDBs|Special Purpose DBs f9be6cb6c892febdd57719a59cc16546d93cf31a 2484 2483 2010-06-11T19:49:42Z TerryDisz 4 wikitext text/x-wiki * Navigation ** Home_of_the_SEED|Home of the SEED ** Annotating_1000_genomes|Manifesto ** SEED_People| SEED People ** Contact| Contact * SEEDs ** http://seed-viewer.theseed.org/|SEED-Viewer ** http://theseed.uchicago.edu/FIG/index.cgi|Public-SEED * Applications ** http://servers.nmpdr.org/|Network-Based SEED API ** http://blog.theseed.org/servers/|Servers Blog ** http://rast.nmpdr.org/|RAST Annotation Server ** http://metagenomics.nmpdr.org/|Metagenomics RAST Server * Documentation ** http://www.nmpdr.org/FIG/wiki/view.cgi/Main/RAST|RAST Server Tutorial ** http://www.nmpdr.org/FIG/wiki/view.cgi/Main/MG-RAST|MG-RAST Tutorial ** SEED_Viewer_Tutorial|SEED Viewer Tutorial * Miscellaneous ** DownloadPage|Download Page ** http://www.nmpdr.org/FIG/wiki/view.cgi/Main/FAQS|FAQ Frequently Asked Questions ** Glossary|Glossary ** SOPs|SOPs ** SpecialPurposeDBs|Special Purpose DBs 938ab63ad34895821ae79a44c7dd670c386afece 0 1382 2472 1491 2009-01-06T15:39:21Z Marland 16 wikitext text/x-wiki == EGGS database: Essential Genes on Genome Scale == SEED maintains an up-to-date database of all microbial gene essentiality data experimentally obtained in the currently published genome-scale gene essentiality screens (listed in Table 1). Comparative analysis of these data across multiple organisms in a rich genomic, biochemical, and phylogenetic contexts provided by the collection of annotated Subsystems greatly facilitates their interpretation and practical applications, such as, understanding of cellular networks, gene and pathway discovery, identification of novel drug targets, and strain engineering. [http://www.nmpdr.org/FIG/wiki/view.cgi/Main/EssentialGenes EGGS Database] 1846d7a481f4144bb7700aa146f958ebddf3d3a0 0 1617 2480 2009-04-27T18:13:50Z FolkerMeyer 2 wikitext text/x-wiki This is the new home of the FIGfams (ALEX is going to make it that) dccb9cd17bc96a1dd3f7961cdc8e2c74fbdb614f 8 1090 2486 2484 2010-08-10T19:11:39Z BruceParrello 19 wikitext text/x-wiki * Navigation ** Home_of_the_SEED|Home of the SEED ** Annotating_1000_genomes|Manifesto ** SEED_People| SEED People ** Contact| Contact * SEEDs ** http://seed-viewer.theseed.org/|SEED-Viewer ** http://theseed.uchicago.edu/FIG/index.cgi|Public-SEED ** http://pseed.theseed.org/|PATRIC SEED * Applications ** http://servers.nmpdr.org/|Network-Based SEED API ** http://blog.theseed.org/servers/|Servers Blog ** http://rast.nmpdr.org/|RAST Annotation Server ** http://metagenomics.nmpdr.org/|Metagenomics RAST Server * Documentation ** http://www.nmpdr.org/FIG/wiki/view.cgi/Main/RAST|RAST Server Tutorial ** http://www.nmpdr.org/FIG/wiki/view.cgi/Main/MG-RAST|MG-RAST Tutorial ** SEED_Viewer_Tutorial|SEED Viewer Tutorial * Miscellaneous ** DownloadPage|Download Page ** http://www.nmpdr.org/FIG/wiki/view.cgi/Main/FAQS|FAQ Frequently Asked Questions ** Glossary|Glossary ** SOPs|SOPs ** SpecialPurposeDBs|Special Purpose DBs 95805d18ce5d1671be2c1530d73e6c264a7586b0 2487 2486 2010-08-10T19:14:43Z BruceParrello 19 wikitext text/x-wiki * Navigation ** Home_of_the_SEED|Home of the SEED ** Annotating_1000_genomes|Manifesto ** SEED_People| SEED People ** Contact| Contact * SEEDs ** http://seed-viewer.theseed.org/|SEED-Viewer ** http://theseed.uchicago.edu/FIG/index.cgi|Public-SEED ** http://pseed.theseed.org/|PATRIC SEED * Applications ** http://blog.theseed.org/servers/|Network-Based SEED API ** http://rast.nmpdr.org/|RAST Annotation Server ** http://metagenomics.nmpdr.org/|Metagenomics RAST Server * Documentation ** http://www.nmpdr.org/FIG/wiki/view.cgi/Main/RAST|RAST Server Tutorial ** http://www.nmpdr.org/FIG/wiki/view.cgi/Main/MG-RAST|MG-RAST Tutorial ** SEED_Viewer_Tutorial|SEED Viewer Tutorial * Miscellaneous ** DownloadPage|Download Page ** http://www.nmpdr.org/FIG/wiki/view.cgi/Main/FAQS|FAQ Frequently Asked Questions ** Glossary|Glossary ** SOPs|SOPs ** SpecialPurposeDBs|Special Purpose DBs 6b49b7192e6718999365cfbb3d45de39d785cdcb 2488 2487 2010-08-12T19:49:49Z BruceParrello 19 wikitext text/x-wiki * Navigation ** Home_of_the_SEED|Home of the SEED ** Annotating_1000_genomes|Manifesto ** SEED_People| SEED People ** Contact| Contact * SEEDs ** http://seed-viewer.theseed.org/|SEED-Viewer ** http://theseed.uchicago.edu/FIG/index.cgi|Public-SEED ** http://pseed.theseed.org/|PATRIC SEED * Applications ** http://blog.theseed.org/servers/|Servers Blog ** http://rast.nmpdr.org/|RAST Annotation Server ** http://metagenomics.nmpdr.org/|Metagenomics RAST Server * Documentation ** http://www.nmpdr.org/FIG/wiki/view.cgi/Main/RAST|RAST Server Tutorial ** http://www.nmpdr.org/FIG/wiki/view.cgi/Main/MG-RAST|MG-RAST Tutorial ** SEED_Viewer_Tutorial|SEED Viewer Tutorial * Miscellaneous ** DownloadPage|Download Page ** http://www.nmpdr.org/FIG/wiki/view.cgi/Main/FAQS|FAQ Frequently Asked Questions ** Glossary|Glossary ** SOPs|SOPs ** SpecialPurposeDBs|Special Purpose DBs 85dcc64996749b3d39c14ff57973910bf5b040ee 2489 2488 2010-08-12T20:32:29Z BruceParrello 19 wikitext text/x-wiki * Navigation ** Home_of_the_SEED|Home of the SEED ** Annotating_1000_genomes|Manifesto ** SEED_People| SEED People ** Contact| Contact * SEEDs ** http://seed-viewer.theseed.org/|SEED-Viewer ** http://theseed.uchicago.edu/FIG/index.cgi|Public-SEED ** http://pseed.theseed.org/|PATRIC SEED * Applications ** http://blog.theseed.org/servers/|Servers Blog ** http://blog.theseed.org/model_seed/|Model SEED Blog ** http://rast.nmpdr.org/|RAST Annotation Server ** http://metagenomics.nmpdr.org/|Metagenomics RAST Server * Documentation ** http://www.nmpdr.org/FIG/wiki/view.cgi/Main/RAST|RAST Server Tutorial ** http://www.nmpdr.org/FIG/wiki/view.cgi/Main/MG-RAST|MG-RAST Tutorial ** SEED_Viewer_Tutorial|SEED Viewer Tutorial * Miscellaneous ** DownloadPage|Download Page ** http://www.nmpdr.org/FIG/wiki/view.cgi/Main/FAQS|FAQ Frequently Asked Questions ** Glossary|Glossary ** SOPs|SOPs ** SpecialPurposeDBs|Special Purpose DBs 5fca033a4449d508f7e9f3bc4de52a244ad30d0d 2490 2489 2010-08-18T19:23:03Z BruceParrello 19 wikitext text/x-wiki * Navigation ** Home_of_the_SEED|Home of the SEED ** Annotating_1000_genomes|Manifesto ** SEED_People| SEED People ** Contact| Contact * SEEDs ** http://seed-viewer.theseed.org/|SEED-Viewer ** http://theseed.uchicago.edu/FIG/index.cgi|Public-SEED ** http://pseed.theseed.org/|PATRIC SEED * Applications ** http://blog.theseed.org/servers/|Servers Blog ** http://blog.theseed.org/model_seed/|Model SEED Blog ** http://rast.nmpdr.org/|RAST Annotation Server ** http://metagenomics.nmpdr.org/|Metagenomics RAST Server ** http://blog.theseed.org/servers/2010/07/scan-for-matches.html Scan for Matches (patscan) * Documentation ** http://www.nmpdr.org/FIG/wiki/view.cgi/Main/RAST|RAST Server Tutorial ** http://www.nmpdr.org/FIG/wiki/view.cgi/Main/MG-RAST|MG-RAST Tutorial ** SEED_Viewer_Tutorial|SEED Viewer Tutorial * Miscellaneous ** DownloadPage|Download Page ** http://www.nmpdr.org/FIG/wiki/view.cgi/Main/FAQS|FAQ Frequently Asked Questions ** Glossary|Glossary ** SOPs|SOPs ** SpecialPurposeDBs|Special Purpose DBs 8b05afbcd9e47e842e832466db7c90bac9cc002b 2491 2490 2010-08-18T19:24:46Z BruceParrello 19 wikitext text/x-wiki * Navigation ** Home_of_the_SEED|Home of the SEED ** Annotating_1000_genomes|Manifesto ** SEED_People| SEED People ** Contact| Contact * SEEDs ** http://seed-viewer.theseed.org/|SEED-Viewer ** http://theseed.uchicago.edu/FIG/index.cgi|Public-SEED ** http://pseed.theseed.org/|PATRIC SEED * Applications ** http://blog.theseed.org/servers/|Servers Blog ** http://blog.theseed.org/model_seed/|Model SEED Blog ** http://rast.nmpdr.org/|RAST Annotation Server ** http://metagenomics.nmpdr.org/|Metagenomics RAST Server ** http://blog.theseed.org/servers/2010/07/scan-for-matches.html| Scan for Matches (patscan) * Documentation ** http://www.nmpdr.org/FIG/wiki/view.cgi/Main/RAST|RAST Server Tutorial ** http://www.nmpdr.org/FIG/wiki/view.cgi/Main/MG-RAST|MG-RAST Tutorial ** SEED_Viewer_Tutorial|SEED Viewer Tutorial * Miscellaneous ** DownloadPage|Download Page ** http://www.nmpdr.org/FIG/wiki/view.cgi/Main/FAQS|FAQ Frequently Asked Questions ** Glossary|Glossary ** SOPs|SOPs ** SpecialPurposeDBs|Special Purpose DBs c3cec90e1f120907e21f3c6dd9f553ee822e8b81 2492 2491 2010-11-15T22:27:43Z TerryDisz 4 wikitext text/x-wiki * Navigation ** Home_of_the_SEED|Home of the SEED ** Annotating_1000_genomes|Manifesto ** SEED_People| SEED People ** Contact| Contact * SEEDs ** http://seed-viewer.theseed.org/|SEED-Viewer ** http://theseed.uchicago.edu/FIG/index.cgi|Public-SEED ** http://pseed.theseed.org/|PATRIC SEED * Applications ** http://blog.theseed.org/servers/|Servers Blog ** http://blog.theseed.org/model_seed/|Model SEED Blog ** http://seed-viewer.theseed.org/seedviewer.cgi?page=ModelView Model SEED ** http://rast.nmpdr.org/|RAST Annotation Server ** http://metagenomics.nmpdr.org/|Metagenomics RAST Server ** http://blog.theseed.org/servers/2010/07/scan-for-matches.html| Scan for Matches (patscan) * Documentation ** http://www.nmpdr.org/FIG/wiki/view.cgi/Main/RAST|RAST Server Tutorial ** http://www.nmpdr.org/FIG/wiki/view.cgi/Main/MG-RAST|MG-RAST Tutorial ** SEED_Viewer_Tutorial|SEED Viewer Tutorial * Miscellaneous ** DownloadPage|Download Page ** http://www.nmpdr.org/FIG/wiki/view.cgi/Main/FAQS|FAQ Frequently Asked Questions ** Glossary|Glossary ** SOPs|SOPs ** SpecialPurposeDBs|Special Purpose DBs c8e4c3dcdae259d6386e8193f94331a0f7bd0d2a 2493 2492 2010-11-15T22:29:31Z TerryDisz 4 wikitext text/x-wiki * Navigation ** Home_of_the_SEED|Home of the SEED ** Annotating_1000_genomes|Manifesto ** SEED_People| SEED People ** Contact| Contact * SEEDs ** http://seed-viewer.theseed.org/|SEED-Viewer ** http://theseed.uchicago.edu/FIG/index.cgi|Public-SEED ** http://pseed.theseed.org/|PATRIC SEED * Applications ** http://blog.theseed.org/servers/|Servers Blog ** http://blog.theseed.org/model_seed/|Model SEED Blog ** http://seed-viewer.theseed.org/models SEED ** http://rast.nmpdr.org/|RAST Annotation Server ** http://metagenomics.nmpdr.org/|Metagenomics RAST Server ** http://blog.theseed.org/servers/2010/07/scan-for-matches.html| Scan for Matches (patscan) * Documentation ** http://www.nmpdr.org/FIG/wiki/view.cgi/Main/RAST|RAST Server Tutorial ** http://www.nmpdr.org/FIG/wiki/view.cgi/Main/MG-RAST|MG-RAST Tutorial ** SEED_Viewer_Tutorial|SEED Viewer Tutorial * Miscellaneous ** DownloadPage|Download Page ** http://www.nmpdr.org/FIG/wiki/view.cgi/Main/FAQS|FAQ Frequently Asked Questions ** Glossary|Glossary ** SOPs|SOPs ** SpecialPurposeDBs|Special Purpose DBs 7bef3b5c602816cdc873845bec784b76466f12da 2494 2493 2010-11-15T22:31:01Z TerryDisz 4 wikitext text/x-wiki * Navigation ** Home_of_the_SEED|Home of the SEED ** Annotating_1000_genomes|Manifesto ** SEED_People| SEED People ** Contact| Contact * SEEDs ** http://seed-viewer.theseed.org/|SEED-Viewer ** http://theseed.uchicago.edu/FIG/index.cgi|Public-SEED ** http://pseed.theseed.org/|PATRIC SEED * Applications ** http://blog.theseed.org/servers/|Servers Blog ** http://blog.theseed.org/model_seed/|Model SEED Blog ** http://seed-viewer.theseed.org/models| SEED ** http://rast.nmpdr.org/|RAST Annotation Server ** http://metagenomics.nmpdr.org/|Metagenomics RAST Server ** http://blog.theseed.org/servers/2010/07/scan-for-matches.html| Scan for Matches (patscan) * Documentation ** http://www.nmpdr.org/FIG/wiki/view.cgi/Main/RAST|RAST Server Tutorial ** http://www.nmpdr.org/FIG/wiki/view.cgi/Main/MG-RAST|MG-RAST Tutorial ** SEED_Viewer_Tutorial|SEED Viewer Tutorial * Miscellaneous ** DownloadPage|Download Page ** http://www.nmpdr.org/FIG/wiki/view.cgi/Main/FAQS|FAQ Frequently Asked Questions ** Glossary|Glossary ** SOPs|SOPs ** SpecialPurposeDBs|Special Purpose DBs 7ccc0fa5a4b56b10d7ba51af69c80c28cc0369e4 2495 2494 2010-11-15T22:31:37Z TerryDisz 4 wikitext text/x-wiki * Navigation ** Home_of_the_SEED|Home of the SEED ** Annotating_1000_genomes|Manifesto ** SEED_People| SEED People ** Contact| Contact * SEEDs ** http://seed-viewer.theseed.org/|SEED-Viewer ** http://theseed.uchicago.edu/FIG/index.cgi|Public-SEED ** http://pseed.theseed.org/|PATRIC SEED * Applications ** http://blog.theseed.org/servers/|Servers Blog ** http://blog.theseed.org/model_seed/|Model SEED Blog ** http://seed-viewer.theseed.org/models| Model SEED-Viewer ** http://rast.nmpdr.org/|RAST Annotation Server ** http://metagenomics.nmpdr.org/|Metagenomics RAST Server ** http://blog.theseed.org/servers/2010/07/scan-for-matches.html| Scan for Matches (patscan) * Documentation ** http://www.nmpdr.org/FIG/wiki/view.cgi/Main/RAST|RAST Server Tutorial ** http://www.nmpdr.org/FIG/wiki/view.cgi/Main/MG-RAST|MG-RAST Tutorial ** SEED_Viewer_Tutorial|SEED Viewer Tutorial * Miscellaneous ** DownloadPage|Download Page ** http://www.nmpdr.org/FIG/wiki/view.cgi/Main/FAQS|FAQ Frequently Asked Questions ** Glossary|Glossary ** SOPs|SOPs ** SpecialPurposeDBs|Special Purpose DBs e0fb87be961ea64e0703e06985e102453c3c5cf9 2496 2495 2010-11-15T22:34:08Z TerryDisz 4 wikitext text/x-wiki * Navigation ** Home_of_the_SEED|Home of the SEED ** Annotating_1000_genomes|Manifesto ** SEED_People| SEED People ** Contact| Contact * SEEDs ** http://seed-viewer.theseed.org/|SEED-Viewer ** http://theseed.uchicago.edu/FIG/index.cgi|Public-SEED ** http://pseed.theseed.org/|PATRIC SEED * Applications ** http://blog.theseed.org/servers/|Servers Blog ** http://blog.theseed.org/model_seed/|Model SEED Blog ** http://seed-viewer.theseed.org/models|Model SEED Viewer ** http://rast.nmpdr.org/|RAST Annotation Server ** http://metagenomics.nmpdr.org/|Metagenomics RAST Server ** http://blog.theseed.org/servers/2010/07/scan-for-matches.html| Scan for Matches (patscan) * Documentation ** http://www.nmpdr.org/FIG/wiki/view.cgi/Main/RAST|RAST Server Tutorial ** http://www.nmpdr.org/FIG/wiki/view.cgi/Main/MG-RAST|MG-RAST Tutorial ** SEED_Viewer_Tutorial|SEED Viewer Tutorial * Miscellaneous ** DownloadPage|Download Page ** http://www.nmpdr.org/FIG/wiki/view.cgi/Main/FAQS|FAQ Frequently Asked Questions ** Glossary|Glossary ** SOPs|SOPs ** SpecialPurposeDBs|Special Purpose DBs eefbf637a2a869dcddf184699f7a67744fa3077f 2497 2496 2010-11-15T22:35:46Z TerryDisz 4 wikitext text/x-wiki * Navigation ** Home_of_the_SEED|Home of the SEED ** Annotating_1000_genomes|Manifesto ** SEED_People| SEED People ** Contact| Contact * SEEDs ** http://seed-viewer.theseed.org/|SEED-Viewer ** http://theseed.uchicago.edu/FIG/index.cgi|Public-SEED ** http://pseed.theseed.org/|PATRIC SEED ** http://seed-viewer.theseed.org/models|Model SEED * Applications ** http://blog.theseed.org/servers/|Servers Blog ** http://blog.theseed.org/model_seed/|Model SEED Blog ** http://rast.nmpdr.org/|RAST Annotation Server ** http://metagenomics.nmpdr.org/|Metagenomics RAST Server ** http://blog.theseed.org/servers/2010/07/scan-for-matches.html| Scan for Matches (patscan) * Documentation ** http://www.nmpdr.org/FIG/wiki/view.cgi/Main/RAST|RAST Server Tutorial ** http://www.nmpdr.org/FIG/wiki/view.cgi/Main/MG-RAST|MG-RAST Tutorial ** SEED_Viewer_Tutorial|SEED Viewer Tutorial * Miscellaneous ** DownloadPage|Download Page ** http://www.nmpdr.org/FIG/wiki/view.cgi/Main/FAQS|FAQ Frequently Asked Questions ** Glossary|Glossary ** SOPs|SOPs ** SpecialPurposeDBs|Special Purpose DBs 89f0dc022eca2d46e5fcf351b1f310f1ae3bfa6e 2499 2497 2011-02-07T22:31:27Z BobOlson 5 wikitext text/x-wiki * Navigation ** Home_of_the_SEED|Home of the SEED ** Annotating_1000_genomes|Manifesto ** SEED_People| SEED People ** Contact| Contact * SEEDs ** http://seed-viewer.theseed.org/|SEED-Viewer ** http://theseed.uchicago.edu/FIG/index.cgi|UChicago SEED ** http://bio-data-1.mcs.anl.gov/public-pseed/FIG/seedviewer.cgi|PubSEED ** http://pseed.theseed.org/|PATRIC SEED ** http://seed-viewer.theseed.org/models|Model SEED * Applications ** http://blog.theseed.org/servers/|Servers Blog ** http://blog.theseed.org/model_seed/|Model SEED Blog ** http://rast.nmpdr.org/|RAST Annotation Server ** http://metagenomics.nmpdr.org/|Metagenomics RAST Server ** http://blog.theseed.org/servers/2010/07/scan-for-matches.html| Scan for Matches (patscan) * Documentation ** http://www.nmpdr.org/FIG/wiki/view.cgi/Main/RAST|RAST Server Tutorial ** http://www.nmpdr.org/FIG/wiki/view.cgi/Main/MG-RAST|MG-RAST Tutorial ** SEED_Viewer_Tutorial|SEED Viewer Tutorial * Miscellaneous ** DownloadPage|Download Page ** http://www.nmpdr.org/FIG/wiki/view.cgi/Main/FAQS|FAQ Frequently Asked Questions ** Glossary|Glossary ** SOPs|SOPs ** SpecialPurposeDBs|Special Purpose DBs 78de10ef5a60f162a13b1e18b9a62df6468446f1 2501 2499 2011-03-23T21:12:21Z BobOlson 5 wikitext text/x-wiki * Navigation ** Home_of_the_SEED|Home of the SEED ** Annotating_1000_genomes|Manifesto ** SEED_People| SEED People ** Contact| Contact * SEEDs ** http://seed-viewer.theseed.org/|SEED-Viewer ** http://theseed.uchicago.edu/FIG/index.cgi|UChicago SEED ** http://pubseed.theseed.org/|PubSEED ** http://pseed.theseed.org/|PATRIC SEED ** http://seed-viewer.theseed.org/models|Model SEED * Applications ** http://blog.theseed.org/servers/|Servers Blog ** http://blog.theseed.org/model_seed/|Model SEED Blog ** http://rast.nmpdr.org/|RAST Annotation Server ** http://metagenomics.nmpdr.org/|Metagenomics RAST Server ** http://blog.theseed.org/servers/2010/07/scan-for-matches.html| Scan for Matches (patscan) * Documentation ** http://www.nmpdr.org/FIG/wiki/view.cgi/Main/RAST|RAST Server Tutorial ** http://www.nmpdr.org/FIG/wiki/view.cgi/Main/MG-RAST|MG-RAST Tutorial ** SEED_Viewer_Tutorial|SEED Viewer Tutorial * Miscellaneous ** DownloadPage|Download Page ** http://www.nmpdr.org/FIG/wiki/view.cgi/Main/FAQS|FAQ Frequently Asked Questions ** Glossary|Glossary ** SOPs|SOPs ** SpecialPurposeDBs|Special Purpose DBs 4f1cba13cec3de7bda74f69bc8ce0de3604b4a9d 2511 2501 2014-05-02T02:50:52Z GDPusch 27 Updated the sidebar to add an entry for "Other SEED/RAST Tutorials" wikitext text/x-wiki * Navigation ** Home_of_the_SEED|Home of the SEED ** Annotating_1000_genomes|Manifesto ** SEED_People| SEED People ** Contact| Contact * SEEDs ** http://seed-viewer.theseed.org/|SEED-Viewer ** http://theseed.uchicago.edu/FIG/index.cgi|UChicago SEED ** http://pubseed.theseed.org/|PubSEED ** http://pseed.theseed.org/|PATRIC SEED ** http://seed-viewer.theseed.org/models|Model SEED * Applications ** http://blog.theseed.org/servers/|Servers Blog ** http://blog.theseed.org/model_seed/|Model SEED Blog ** http://rast.nmpdr.org/|RAST Annotation Server ** http://metagenomics.nmpdr.org/|Metagenomics RAST Server ** http://blog.theseed.org/servers/2010/07/scan-for-matches.html| Scan for Matches (patscan) * Documentation ** http://www.nmpdr.org/FIG/wiki/view.cgi/Main/RAST|RAST Server Tutorial ** http://www.nmpdr.org/FIG/wiki/view.cgi/Main/MG-RAST|MG-RAST Tutorial ** SEED_Viewer_Tutorial|SEED Viewer Tutorial ** http://www.theseed.org/tutorials/ |Other SEED/RAST tutorials * Miscellaneous ** DownloadPage|Download Page ** http://www.nmpdr.org/FIG/wiki/view.cgi/Main/FAQS|FAQ Frequently Asked Questions ** Glossary|Glossary ** SOPs|SOPs ** SpecialPurposeDBs|Special Purpose DBs 2a59c4d2d79606771da255c47b65b69e42e51dae 2513 2511 2014-05-02T02:51:25Z GDPusch 27 wikitext text/x-wiki * Navigation ** Home_of_the_SEED|Home of the SEED ** Annotating_1000_genomes|Manifesto ** SEED_People| SEED People ** Contact| Contact * SEEDs ** http://seed-viewer.theseed.org/|SEED-Viewer ** http://theseed.uchicago.edu/FIG/index.cgi|UChicago SEED ** http://pubseed.theseed.org/|PubSEED ** http://pseed.theseed.org/|PATRIC SEED ** http://seed-viewer.theseed.org/models|Model SEED * Applications ** http://blog.theseed.org/servers/|Servers Blog ** http://blog.theseed.org/model_seed/|Model SEED Blog ** http://rast.nmpdr.org/|RAST Annotation Server ** http://metagenomics.nmpdr.org/|Metagenomics RAST Server ** http://blog.theseed.org/servers/2010/07/scan-for-matches.html| Scan for Matches (patscan) * Documentation ** http://www.nmpdr.org/FIG/wiki/view.cgi/Main/RAST|RAST Server Tutorial ** http://www.nmpdr.org/FIG/wiki/view.cgi/Main/MG-RAST|MG-RAST Tutorial ** SEED_Viewer_Tutorial|SEED Viewer Tutorial ** http://www.theseed.org/tutorials/ |Other SEED/RAST Tutorials * Miscellaneous ** DownloadPage|Download Page ** http://www.nmpdr.org/FIG/wiki/view.cgi/Main/FAQS|FAQ Frequently Asked Questions ** Glossary|Glossary ** SOPs|SOPs ** SpecialPurposeDBs|Special Purpose DBs 87c472a2f54694fd45e85e7fdf2a6afd064a509d 0 1433 2503 1848 2012-06-21T17:58:13Z BobOlson 5 Replaced content with "Please see [http://blog.metagenomics.anl.gov/ the MG-RAST blog] for current information about MG-RAST." wikitext text/x-wiki Please see [http://blog.metagenomics.anl.gov/ the MG-RAST blog] for current information about MG-RAST. 4f0443618beee39666460210b0b85f3a0cf1f55f 0 1375 2505 2456 2012-06-21T21:07:17Z BobOlson 5 wikitext text/x-wiki Have questions or comments about our applications? '''RAST''' Email: [mailto:rast@mcs.anl.gov] ""Model SEED"" Email: [mailto:model@theseed.org] '''Metagenomics RAST''' Email: [mailto:mg-rast@mcs.anl.gov] '''The SEED''' Email: [mailto:info@theseed.org] 81566088139794a0fa57afb4d47bc53c4ce15712 2507 2505 2012-06-21T21:07:38Z BobOlson 5 wikitext text/x-wiki Have questions or comments about our applications? '''RAST''' Email: [mailto:rast@mcs.anl.gov] '''Model SEED''' Email: [mailto:model@theseed.org] '''Metagenomics RAST''' Email: [mailto:mg-rast@mcs.anl.gov] '''The SEED''' Email: [mailto:info@theseed.org] 52d02a7a63bf0087294bde369292a2d6af7b47af 2509 2507 2012-06-21T21:07:59Z BobOlson 5 wikitext text/x-wiki Have questions or comments about our applications? '''RAST''' Email: [mailto:rast@mcs.anl.gov] '''Model SEED''' Email: [mailto:model@theseed.org] '''Metagenomics RAST''' Email: [mailto:mg-rast@mcs.anl.gov] '''The SEED''' Email: [mailto:info@theseed.org] 97c6a034445bc9db63edf887f5edb3abe5926211